BROOKHAVEN NATIONAL LABORATORY

PROTEIN DATA BANK

NEWSLETTER

May, 1977Number 4

A number of important developments have occurred since we distributedour last newsletter six months ago. All atomic coordinate entries in the DataBank have now been converted to the 80-character format, and henceforth only80-character entries will be distributed. This will make distribution tapesmore compact, and generally should simplify processing for recipients.The size of the Data Bank has continued to increase, and we now have availablefor distribution a total of 77 coordinate entries for 47 different macro-molecules. A current list of atomic coordinate holdings, with identificationcodes to be used in requesting data, is shown in Table 1. In addition, certainnon-standard entries, containing structure factor-phase information and torsionangles, are available. These are shown in Table 2.

We have combined our mailing lists, and beginning with this issue,Brookhaven will mail newsletters directly to all users worldwide. Datadistribution is divided geographically as follows: Brookhaven will handlethe Americas, the University of Tokyo will handle Japan, and CambridgeUniversity will distribute within Europe and worldwide. The request formincluded with this newsletter has been preaddressed to the center that handlesyour area. Please use this form to request data or copies of documentation.Data requests directed to Brookhaven should include a check or purchase orderfor U.S. $34.30, made to the order of Brookhaven National Laboratory, to coverpostage and handling. This charge is subject to increases in the future.Requests should be accompanied by a new 2400' reel of magnetic tape. In theevent it is not possible for the user to supply a tape, Brookhaven can do soat a total cost of $47.00. Cambridge and Tokyo presently distribute data freeof charge.

Errors occasionally are found in data deposited with the Bank, andcorrections and revisions are submitted by depositors or approved by them. Wehave compiled a list of corrections and revisions of the master file appliedsince June 1976, and this list is attached as Table 3.

As the size of the Data Bank increases, possibilities for interactiveaccess become more attractive. Brookhaven recently has agreed to make portionsof the file available through the NIH/EPA Chemical Information System (CIS) .The CIS presently includes the Cambridge Bibliographic and Structural Data Filesfor organic and organometallic compounds. These data may be accessed within theU.S. via

CYPHERNET,

a commercial timesharing network. Initially, we plan tomake available through CIS the Protein Data Bank bibliographic and sequenceinformation, together with identification codes for the various entries, indexcitations to AMSOM (R. J. Feldmann, Atlas of Macromolecular Structure on Micro-fiche, Tracor Jitco Inc., Rockville MD, 1976, ISBN 0-9179 34-01-6), and certainother descriptive material. This interactive capability should be implementedbefore the end of 1977.

1

TABLE 1. PROTEIN DATA BONK ATOMIC COORDINATE HOLDINGS10-MAY-77

IDENT DATEXCODE MOLECULE DEPOSITOR STATUS2ADK ODENYLA TE

KINASE

G SCHULZ 3X77 RIADH ALCOHOL DEHYDROGENASE (APP-RIR) C -I. RRONDEN 8X762ADH OLLOHOL DEHYDROGENASE (ORTHOPHEN) C -1. BRANDEN 8X76IBCL

BACIEkIOCHLOPOPHYIL

A-PROTE IN(CGRE ONLY)B MATTHEUS 3x77ICPV CALCIUM-BINDING PARVALBUMIN SET 6A F KRETSINGER 8X742CPV

CALCIUM-BINDING

PARVALBUMIN SET 6H R KRETSINGER 8X743CFV CALCIUM-BINDING FARVALBUMIN SET 61 R. KRETSINGER 8X74ICAB CARBONIT HHHYPRASE B K. KANNON 6x76ILAC IARBONIC AHHYPRASE C K. KONNON 5X76ICPA

CARBOXYPEPTIDBSE

A U. LIPSCOMB 2X732CHA

ALPHA-CHYTETRYPSIN

(TOSYL) D. BLOU 1x75 R3CHA HLPHA-CIIrMOTRYPSIN A. TULINSKY 8x76iLCH

GBMMO-CHYMOTRYPSIN

COHEN. DAVIES. SILVERTON 2X77ICHG

CHYMOTPYPSINOGEN

J. KRAUT

3,75

-_2 r___ _M!i 5 REEKt " BECKER. EDELMBN 4X75iCNrt

CUNCANAVALIN

A K. HARDMAN 9X76 RIBSC CYTOCHROME B5 F. S. MATHEUS 8X72ILYT

CYTOCHROME

C (ALBACORE. OXIDIZED) R. DICKFRSUN 9X762CYT

CYTOCHROME

C (ALBACORE. REDUCED) R. DICKERSON 9x76ICYC

CYTOCHROME

C (BONITO. HEART) M. KOKUDO B/76IC2C CYTOCHRCIE C2J. KRAUT 1x73IS E,"'T?fH?PME Css° R - TIMXOVICH 8X76lEST FLASIHSE H. UATSON 5/76IFDX FEPREDOXIN L. JENSEN g/76IFXN FLAVODOXIN (CLOSTRIDIUM MP) M. LUDUIG 11X74IGFD GL _ERALDEHYDE-3-P-DEHYDROGENASE(LOBSTR)M. ROSSMANN 7X7521-HB

HEMOGLOBIN

(HORSE. AOUO MET) LADNER. HEIDNER. PERUTZ 2X77 RIDHB HEMOGLOBIN (HORSE. DEOXY) M. PEROTZ. G. FERMI 11X73IHHE HEMOGLOBIN (HUMAN. DEOXY) M. PERUTZ. G FFRMI 4X75IFDH HEMOGLOBIN (HUMAN. FETAL. DEOXY) J. FRIER

"

8X76ILHB HEMOGLOBIN (LAMPREY) HENDRICKSON. LOVE- KARLE 3X73IYHX HE .KINASE (YEAST) 01 I 1 T. STEITZ 1x76 BIHIP HIGH

TOTENTIAL

IPOH PROTEIN J. KRAUT 4X75IFAB

IMMUNOGLOBULIN

FOU' (NEU) R. POLJAK 8X76IREI

IItUNOGLOBULIN

B-J FRAGMENT PE I 0. EPP. R. HUBER 3X764LDH LOCTOTE DEHYDROGENASE U. EVENTOFF. M. ROSSMANN 4x77 R3LDH LOCTOTE DEHYDROGEHOSExNADXPYRUVATE M. ROSSMANN 1 1X74 DILZM LYSOZYtE (BACTERIOPHAGE T4) B.

MATTHEUS

3x77ILYZ LYSO7YME (HEN EGG-UHITE. SET U2) R. DIAMOND. D. PHILLIPS 2x752LYZ LYSOZYTE (HEN EGG-LKITE. SET RSSD) R. DIAMOND. D. PHILLIPS 2X753LYZ LYSOZYME (HEN

EGG-I.HITE.

SET RS6A) R. DIAMOND. D. PHILLIPS 2x754LYZ LYSOZYMC (HEN EGG-UHITC. SET RS9A) R. DIAMOND. D PHILLIPS 2X75SLYZ

LYSOZYME

(HEN

EGG-UHITE.

SET RSI2A) R. DIAMOND. D. PHILLIPS 2X756LYZ LYSOZYME (HFN EGG UHITE. SET RSI6) R. DIAMOND. D.

PHILLIPS

2X75.-L-iZ

LYSOZYME

(HEN EGG-UHITE. TRICLINIC) A. YONATH 5X77 PIMDH MALATE DEHYDROGENASE L. BANASZAK 6x76 0IMBN MYOGLOBIN .SPERM LHALE) H. UATSON 4X732MBN MYOGLOBIN "SPERM UHhLE. MET) T. TAKAHO 9x76SMRN MYOGLOBIN (SPERM IJHALE. DEOXY) T. TAKANO 9X76BPAP PAPHIN. NATIVE J. DRENTH 11X76 RIPHD POFAIH (ACE-ALA-ALA-PHE-HLA. CYS-25) J. DRENTH 11X76 R2PAD PAPAIN (CYS DtR IV OF CYS-25) J. DRENTH 1/76 R3PAD PAPAIN 'OXIDIZED CYS-25) J. DRENTH 11X76 R■ IPOD PAPAIN (TOS-LYS. CYS-25) J. DRENTH X76 RSPOD PHPAIN (BZOXY-GLY-PHE-GLY. CYS-25) J. DREHTH 11X76 R6PAD PAPAIN (BZOXY-PHE-ALA. CYS-25) J. DRENTH X_RIPGK

PHOSPHOGLYCFRATE

KINASE (YEAST) H. UATSON 5X_ 02PGK

PHOSPHOGLYCERATE

KINASE (HORSE) P. EVANS. D

PHILLIPS

9x76 BIFHB PREALBUMIN (HUMAN. PLASMA) S. OATLEY. D. PHILI IP S 8X76IRNS PIBONUCLEASE S H. L_KOFF 4X732R_ PUBPEDOXIH L.

JENSEN

7x75 nISNS STAPHYLOCOCCAL NUCLEASE F. A. COTTON. E. HAZEN 4X73!SGB STREPTOMYtES GRISEUS PROTEINASE B M. JAMES

5,

76 0

l_B

STREPTOMt'CES GRISEUS PROTEINASE B M. JA _S 5/76 aISBT SUBTIL ISIN BPN' J. KRAUT 8x722SBT SUBTIL ISIN NOVO j. DRENTH 1x76ISOD SUPEROXIDE DISMITOSE J. AND D RICHARDSON 8x75

Q

ITLH THERrOLYSIH (UNRFFINED) B. MPTTHEUS 4X752TLII THERIOLYSIN (REFINED) B. _TTHEUS 4X75

ISRX THIOREDOXIN

8.-O. SODERBCRG 5/7S AIIHA

TRANSFER

RNA < '.EAST. J.

SUSSMAN.

S.-H. KIM 12x752TNA TRANSFER RNA (YEBST. PHE) M.

SUNDARAL

INGAM SX?! D3TNA TPAIISFEP RNA (YEAST. PHE) JACK. LADNER. KLUG 2x77 NI TIM TRIOSE PHOSPHATE

ISOMERASE

I. UILSON. D PHILLIPS 9X76IPTN TRYPSIN (NATIVE. PHB) FEHLHArTER BODE S__r.Fß 1X772PTB

TR'.PSItKBLNZOMIDINE

INHIBITED. PH7) FEHLHAMER. BODE^ SCHLBGER X77 RIFTC TRYPSIN TRYPSIN INHIBITOR COMPLEX

BODEETAL

=(-hl_,_

wr,

X3PTI

TRYPSIN

INHIBITOR (BOVINE. PANCREAS) R. HUBER 76 RJHII

IKiFSIN INHIBITOR

(BOVINE. PANCREAS) R. HUBER 76 RIPTP

TRYPSIN

'DIP INHIBITED) J. CHAMBERS. R. STROUD 3x77

TfIBLE 2. PROTEIN DATA BANK NON-STANDARD ENTRIES

18-MHY-77

IDPNT DATEXCOW MOLECULE

DEPOSITOR

CODECHYMOF

ALPHA-CHYMOTRYPSIN

(TOSYL) D. BLOU 4/73 SFRCARPB4

CALCIUM-BINDING

PARVALBUMIN R. KRETSINGER 2x74 SFSE&KII,

CALCIUM-BINDING

PARVALBUMIN R.

KRETSINGER

2x74 SF

RCYTBSB2CYTOCHROME

BS F. S .THEUS 5x73 TA

RTUNOX2BI

CYTOCHROME C (OLBACORE. OXIDIZED) R. DICKERSON 5X76 SFKIUNU

_01 CYTOCHROME C

(ALBACORE. OXIDIZED) R. DICKERSON 5X76 SFRTUNRDZBI CYTOCHRO _ C (ALBACORE. REDUCED) R. DICKERSON 5 '76 SF£__ B1 EYyF_o,t C558 R - TI_CVICH 4>76 SFKLYLbbBI CYTUCHRO . CSSA R. TI_CVICH 4.-76 SFRGPDB4 GL YCERAI

DEHYDE-3-P-DEHYDROGENASE

(LOBSTR)M. ROSSmNH 8x75 SFRHUMDEHB2

HEMOGLOBIN

(HUMAN.DEOXY) N. PEPUT2. G FERMI 5X75 SFLArPRYI HEMOGLOBIN (LAMPREY)

HENDRICKSON

LOVE KARLE 5X73 SF

RLDIIO6

LACTATE DEHYDROGENASE M ROSSMANN sx7§ IfRLDKB7 LACTATE

DEHYDROGENASEXNBDXPYRUVATE

M. ROSSMANN 8X75 SFRrETMYSFI MYOGLOBIN (SPERM LHALE. _T> T. TAKANO 6X76 SFRDEMYSFI MYOGLOBIN (SPERM LHALE. DEOXY) T. TAKANO 6/7G SFRRUBYB2

RUBREDOXIN

_. JENSEN 3X74 SFTOkSNABI

TORSION

ANGLES (II PROTEINS) 1 . UU. E KABOT 5/73 TOCODES

SF STRUCTURE FACTORSTA TORSION ANGLES

"NOTE*

IN SOrt CASES. MORE RECENT TORSION ANGLES THAN THOSE CONTAINED IN THEApOVE ENTRIES MAY BE CALCULATED FROM THE APPROPRIATE ATOMIC COORDINATEtnlKltb LlblcD In TflßLc 1.

_.ol__H2!D_

___HI_

o

-.

1_lI

STATUS CODESBLANK STANDARD ENTRY AVAILABLE FOR DISTRIBUTIONA HI PHA

CARBON

ATOMS ONLYB BACKBONE ONLYD NEU DATA HAS BEEN PROMISEDN NEW ENTRY' IJITH DFPOSITOR FOP APPROVALP IN

PPEFhFAIION

R

REPLACES

HH OUT-OF-DATE PARAMETER SET

1

_

%

__HH_19

a25

-.

IUJI

TABLE 3. CORRECTIONS AND REVISIONS OF ATOMIC

COORDINATE

DATA21-APR-77

♦IDENT.IIENA

HEHDER

'

OXYGEN STORAGE 85-APR-73 IMBN

♦

IDEUT. IADI AHEADER ' YsANSCERASEiPHOSPHOjPHOSPHORYL ACCEPTOR 11-JUN-76 IADKAUTHOR

'

G.E. SCHULZ. Ml. ELZINGA. F. MARX AND R.H. SCHIRMER'DELETE. IAD! .8REMBRI 1 PEFERENCE 1. G.E. SCHULZ. Ml. ELZINGA. F. MARX AND R.H.♦DELETE. IAD) .3REMAP) 1 SCHIRMER. THREE-DIMENSIONAL STRUCTURE OF ADENYLATE KINASE.

REMARK ' I COMPARISON OF ADENYLATE KINASE UITH OTHER PROTEINS. NATURE.PEmP. 'TpEFEPENCE 3. G.E. SCHULZ. CD. BARRY. J. FRIEDMAN. P.Y.CHOUPEMhR(

TE '"l 'SECONDARY- STRUCTURE OF ADENLYATE KINASE. NATURE. VOL. 258.

♦

INSERT. lAIiK .27REMARK 5 RESIDUE ASP 65 CHANGED TO GLN 65 AND SEVERAL TYPOGRAPHICALPFIIHPI 5 ERRURS CORRECTED. »NOTE» THE RESIDUE CHANGE MEANS THAT 1REMARK 5 SHOULD BE ADDED TO ALL OTOMI SERIAL NUMBERS PAST RESIDUEREMAP! 5 65. THIS UILL BE COPRECTED _EN THE FULL STRUCTUREPEMAPK 5 BECOMES AVAILABLE. 12-JUL-76REMARK 5SCOPES ' 5 ' 134 APG GLY LYS MET LEU SER GLU ILE MET GLU LYS GLY GLNATOM «B 'CA GUI 65 26.860 21.988 36.888 1.06 0.00

►

IDENT. IADMB♦DELETE. IADK.242MASTER 28 0 6 0 0 0 0 3 194 1 B 15

*lI'ENT. I_3NB*INSERT. IMB. .32PEEIhPK gREMAP- 6 rOPPErTION. THE CONECT 1219 RECORD UAS UPONG. THE 736PETWPI b SHOULD HAVE EEEH. AND IS NOU. 740. 20-SEP-76♦DELETE. II«I . 1334mHECT 121? 740 1220 1225 1236,D|L|TE.,MBN.I379 8 , 8 6 3 2 6 ,268 , m I2"IDENT. ICYCA

♦

INSERT. ICYTI.2IPEMhPI 5REMAPI 5 CORRECTION MADE 25-OCT-76. THE SECOND CONECT RECORD FORPEIBPK 5 hTOII 60S SHOULD HAVE 82? 835 (NOT 819 835)."DELETE. ICYCB94CONEC) 303 82? 835_M. ''"'lf 8 1 5 0 3 8 3 833 1 48 8

*I_EHT,3CHfM3

PEIIAP!'

'

6 CORRECTION. THE CONECT RECORDS UERE INCORRECT. 04-DEC-76

RE_APK 7 COPPECTIDN. CORRECT MASTER RECORD. 03-JRN-77

■DELETE,

3CHAA.I3 „„,„,,, 1733 2 18 .9

"IDENT. ICPAA"INSERT. ICPA.26REMARK 5REMBRK 5 CORRECTION. INSERT MISSING CONECT RECORD. 03-JAN-77"INSERT. ICPA. 2S67CONECT 1277 1119 1276"DELETE. ICPA. 2S7BMBSTER 28 2 1 8 8 32 0 6 2453 2 6

♦

IL'tNl.3LMHH♦INSERT.3CHA. 44REMARK 6REMHPK 6 CORRECTED 04-DEC-76. THE CONECT RECORDS UERE INCORRECT. FCB♦DELETE. 3CHA. IB24. IB23CONECT 6 5 893CONECT 382 301 413CONECT 418 417 302CONECT 333 832 6CONECT 936 985 1445CONECT 1213 1217 1334CONECT 1334 1218 1333CONECT 1383 138^ 1584CONECT 1445 93G 1444CONECT lbB4 1383 1583.DELETE. 3CNA.

,B29

,

,^

0 0 9

,733

2 5 .9

*[DtN!. ILHL.H♦INSERT. ICHG. 43PErWRK 5REMARK 5 CORRECTION. IN RESIDUES TYR 94. TYR 171. AND TYP 228.REMBRK 5 ATOM OH UAS MISNAMED AS 0. UHICH NAME THEREFORE OCCURREDREMBRK 5 TUICE. IT HAS BEEN RENAMED AND RESTORED TO ITS CORRECTREMBRK 5 POSITION AFTER CZ. THUS NECESSITATING RENUMBERING OF THEREMBRK 5 INTERVENING ATOMS CB TAROUGH CZ. 10H FORMERLY HAD SERIALREMBRK 5 NUMBERS 699. 1269.

,66,

AND NOU HAS 706.

,276. ,6bß

REMBRK 5 RESPECTIVELY IN THE THREE TYROSINE RESIDUES.) 03-JAN-77.

ATOMETt '69_ 'cf'" 94 22.52? 15.085 6.574 1.00 0.08

ATOM 700 CG TYR 94

22.6,2 ,5.072 8.,74

1.00 0.00ATOM 701 CDI TYR 94 22.888 16.371 8.687 1.06 8.00ATOM 702 CD2 TYR 94 22.232 13.962 8.963 1.00 8.00ATOM 703 CEI TYR 94 22.882 16.460 9.989 1.00 0.00ATOM 704 CE2 TYR 94 22.418 14.151 10.366 1.00 0.60ATOM 705 CZ TYR 94 22.597 15.449 10.877 1.00 0.00ATOMI 706 OH TYR 94 22.492 15.535 12.378 1.00 0.06

ATDM,

ETE'I269 'C 8 TYR 171 30.355 33.165 18.662 1.06 6.00ATOM 1270 CG TYR

,?,

30.846 34.557

,9.272

1.06 0.80ATOM

,27, CD,

TYR ,7, 36.040 34.545 20.672 1.00 0.00ATOM

,272

CD2 TYR 171 29.552 35.658

,8.580

1.00 0.00ATOM

,273 LE,

TYR

17,

29.830 35.73?

21.38,

1. 00 0.08ATOM 1274 CE2 TYR 171 29.342 36.850 19.289 1.00 0.08ATOM 1275 CZ TYR 171 29.432 36.939 20.690 1.06 8.60ATOM 1276 OH TYR 171 29.026 38.229 21.399 1.86 0.00

«?^ETE iii_ 97"84

228

,9.924

26.607 .2.779 1.00 0.00ATOM 1662 CG TYR 228 19.523 29.191 14.082 1.00 0.06ATOM 1663 CDI TYR 228 20.485 29.896 14.792 1.00 0.00ATOM 1664 CD2 TYR 228 18.259 28.974 14.674 1.00 0.00ATOM 1665 CEI TYR 228 20.182 30.482 16.095 1.00 0.00ATOM 1666 CE2 TYR 228 18.053 29.561 15.879 1.00 0.00ATOM 1667 CZ TYR 228 18.918 30.264 16.588 1.00 0.06ATOM 1668 OH TYR 228 18.712 33.852 17.792 1.86 0.68"DELETE. ICHG. I746 ,MBSTER 44 8 6 2 14 0 0 6 1643 1 10

_DtM I . IL2LH

"INSERT. IC2C.2BREMARK 4REMBRK 4 CORRECTION. IN RESIDUES TYR 46. TYR 48. TYR 52. TYR 70REMBRK 4 AND TYR. 107. ATOM OH UAS MISNAMED AS 0. UHICH NAMEREMBRK 4 THEREFORE OCCURRED TUICE. IT HAS BEEN RENAMED ANDREMBRK 4 RESTORED TO ITS CORRECT POSITION AFTER CZ. THUSREMBRK 4 NECESSITATING RENUMBERING OF THE INTERVENING ATOMS 0REMBRK 4 THROUGH CZ . MOH FORMERLY HAD SERIAL NUMBERS 329. 346.REMBRK 4 3?9. 518. 811 AND NOU HAS 33?. 354. 387. 526. 8.9 INREMBRK 4 THE FIVE TYROSINE RESIDUES.) 03-JAN-77.

ATOM|ETC'329C '084 'TY1« 46 34.163 14.954 35.637 1.00 12.00

ATOM,

330 CB Tffl 46 33.869 12.468 37.615 1.00

,2.00

ATOM!

33,

CG TYR 46 35.385

,1.930

37.554 1.00 12.08

ATOM,

332 CDI TYR 46 36.17? 11.548 36.332 1.00 12.00ATOM! 333 CD2 TYR 46 35.769 11.273 38.651 1.00 12.00ATOM 334 CEI TYR 46 37.553 11.159 36.481 1.00 12.00

ATOM,

335 CE2 TYR 46 37.156 11.172 38.821 1.00 12.00

ATOM,

336 CZ TYR. 46

38.02,

18.823 37.672 1.00

,2.00ATOM,

33? OH TYR 46

39.34, ,0.270

37.803 1.00

,2.00

"DELETE. IC2C.4OI.4O9ATOM 346 0 TYR 48 37.961 14.496 31.332 1.00 13.00ATOMI 347 CB TYR 48 35.422 12.358 32.083 1.00 13.00

ATOM,

348 CG TYR 4B 34.558 11.302 32.752 1.00

,3.00ATOM,

349 CDI TYR 48 35.067 10.095 32.80? 1.00

,3.00

ATOM! 350 CD2 TYR 48 33.942

,1.539

33.976 00

,3.00

ATOM

35, CE,

TYR 48 34.48? 9.084 33.545 1.00

,2.08

ATOM! 352 CE2TYR 48 33.070

10.6,4

34.440 1.00

,3.00

ATOM! 353 CZ TYR 48 33.392

9.32, 34.16,

1.00

,3.00ATOM,

354 OH TYR 48 32.636 8.298 34.683 1.00 13.80"DELETE. 1C2C.434.442ATOM! 379 0 TYR 52 33.398

,0.279

26.862 1.00

,3.08

ATOM! 388 CB TYR 52 35.960

,0.197

29.039 1.00

,3.00ATOM,

381 CG TYR 52 36.95? 8.96? 29.250 1.00

,3.00

ATOM,

382 CDI TYR 52 36.301 7.714 29.514 1.00 13.00

ATOM,

303 CD2 TYR 52

38.5,0

9.144

29,

89 1.00 13.08

ATOM,

384

CE,

TYR 52 37.092

6.6,5

29.860 1.00

,3.00ATOM,

385 CE2 TYR 5? 39.308

7.9,1

29.386 1.00

,3.00ATOM,

386 CZ TYR 52 38.603 6.742 29.934 1.00

,3.00

ATOM 387 OH TYR 52 35.410 5.658 30.564 1.00

,3.00

"DELETE.

1C2C.573.581

ATOM,

516 0 TYR 78 40.160 -.951 28.28? 1.00

,6.00

ATOM 519 CB TYR 78 36.948 -.435 27.636 1.00 16.00

ATOM,

520 CG TYR 70 37.333 .7,5 28.547

,00 ,6.00ATOM,

521

CD,

Til! 70 38. 098 1.591 28.170 1.00 16.00

ATOM,

5?2 CD2 T . 70

37.50,

.394 29 . 868

,06 ,6.00ATOM,

523

CE,

TYU 70

38.7,6

2.407 29.17? 1.00

,6.00ATOM,

524 CE2 TYR ?0 37.809 1.305 30.923 1.00 IC 00ATOM 525 CZ T

»_j

O

__2

J>-

4*I

1

CORRECTIONS AND PEVISIONS OF ATOMIC COORDINATE DATA rCONT. )TABLE 3.21-APP->-77

* IDENT. IFSTA♦DELETE. IEST.34. Ell_ Ft 6PEMAPI. 6 CORRECTION. INSERT MISSING CONECT RECORDS. 03-JAN-77♦INSERT. IEST. I346CONECT 352 231 351

♦

INSERT. IEST. 1948CONECT 1341 1223 1340+IHSEPT.IEST.I3S9CONECT 1466 930 1465CONECT 1613 1400 1612♦DELETE. IEST. I^6IMASTER 23 4 2 2 17 8 1 6 1858 1 19 19

*I DENT. IFABA

♦

INSERT. I FA8. 31REMARK 5REMARI 5 COPPECTION. INSERT MISSING CONECT RECORDS. 03-JAN-77"■INSERT. 1FA8.3297CONECT 608 152 607♦INSERT. IFAB.329BCONECT 1415 963 1414

♦

INSERT. IFAB.33BOCONECT 2297 1716 2296

t INSERT,

IFAB.33BICONECT 3839 2625 3033CONECT 3197 1547 3196tDELETE.IFAB.33O2MASTFR 26 0 0 3 33 0 8 6 3187 2 18 33

♦IDENT.2ADHA♦DELETE. 2ADH. 46REMARK 4 THE CRYSTALLOGRAPHIC

ASYMMETRIC

UNIT OF THIS STRUCTUREREMARK 4 CONTAINS ONE POLYPEPTIDE CHAIN UHICH IS COI"PRI3ED OF TUOREMARK 4 DOMAINS. TO GENERATE COORDINATES FOR THE OTHER CHAIN UHICHREMARK 4 TOMPLETES THE BIOLOGICALLY ACTIVE DIMER THE OPERATIONREMARK 4 GIVEN BELOU fUST 8E APPLIED. NOTE THAT THIS IS A TRUEREMARK 4 CRYSTALLOGRAPHIC DIAD SYTttTRY ELEMENT.REMARK 4 -1.0 0.0 8.8 8.0REMARK 4 0.0 1.0 0.8 0-8REMARK 4 0.0 0.0 -1.0 90.85REMARK 5REMARK 5 CORRECTION. MOVE THE HET CARDS TO THEIR PROPER POSITION.REMARK 5 ALSO INSERT MISSING REMARK 4. 28-MAR-77.

♦

DE1.ETE.2ADH.47.49

♦INSERT,

2ADH. 7BHET ZNI 1 1 CATALYTIC tINCCin lONHET ZN2 2 1 SECOND ZINCCII) lONHET OPH 4 14 ORTHOPHENANTHROLINE♦DELETE. 2ADH. 2962_ASTER 50 8 3 18 22 17 0 6 2801 1 25 29♦IDENT.ICABA♦INSERT.ICAB.2BREMARK 6REMARK 6 CORRECTION. FIX MASTER RECORD TO SHOU CORRECT NUMBER OFKEMARK 6 FTNOTE RECORDS. 28-MAR-77.♦DELETE. ICAB.2I26MASTER 25 10 1 7 18 11 0 6 2024 1 5 21

+IDENT.IFDXAi

INSERT.

IFDX.27REMARK 6REMARK fi CORRECTION. THE SG ATOMS OF CYSTEINES 11. 14. 18.

35, 38,

REMARK b 41. 45 HAD INCORRECT V AND Z COORDINATES. (UHEN THE VALUEREMARK 6 UAS GREATER THAN 9.999 THE HIGH-ORDER DIGIT UAS LOST.)PEMAPK 6 83-TAN-77.♦DELETE. IFDX. I2BATOM 79 SG CYS 11 33.270 10.970 14.503 1.00 0.00♦DELETE. IFDX. I3SATOM 34 SG CYS 14 38.364 5.564 15.917 1.00 8.00♦DELETE. IFDX. I66ATOM 125 SG CYS 18 27.166 .582 21.043 1.00 0.08fDELETE.IFDX.2R9ATOM 248 SG CYS 35 21.379 -.585 18.201 1.08 0.08fDELETF. IFDX.3I IATOM 279 SG CYS 38 22.448 3.239 23.165 1.08 8.88♦DELETE. IFDX.327ATOM 286 SG CYS 41 24. 135 5.893 17.638 1.00 8.86♦DELE 1E. 1FDX.351ATOM 310 SG CYS 45 27.795 11.065 13.311 1.88 0.00♦DELETE. IFDX.4S6mSTEP 18 O 2 0 0 0 8 6 389 I 24 5

♦IDENT. IHIPA♦INSERT.IHIF.4O

PFMAPK 6REMBRK 6 CORRECTION. IN RESIDUE TYR 19. ATOM OH UAS MISNAMED AS 0.PEMAPK 6 WHICH NAME THEREFORE OCCURRED TUICE. IT HAS BEEN RENAMEDPEMAPI 6 AND RESTORED TO ITS CORRECT POSITION AFTER CZ. THUSREMARK 6 NECESSITATING RENUMBERING OF THE INTERVENING ATOMS 0REMARK 6 THROUGH CZ. (OH FORMERLY HAD SERIAL NUMBER 120 AND NOUREMARK 6 HAS 123.) BNL 03-JAN-77.

♦

DELETE. IHIP. 177. 135ATi.l 129 0 TYR 19 22.870 10.840 13.970 1.00 0.80ATOM 121 CB TYR 19 19.860 1 1.020 12.910 1 .80 0.88ATOM 122 CG T~ iT? 19 19.450 1 1.400 14.348 1 . 80 0.00ATOM 123 CDI TYP 19 18.640 12.540 14.528 1 . 08 8.88ATOM 124 CD2 TYR 19 19.928 10.710 15.430 1.00 8.90ATOM 125 CEI TYP 19 18.260 12.910 15.880 1.00 8.08ATOM 126 CE2 TYR 19 19.558 11.070 16.770 1.00 8.00ATOM 127 CZ TYR 19 18.750 12.210 16.920 1.00 0.00ATOM 128 OH TYR 19 18.410 12.580 18.218 1. 60 0 . 08

♦

DELETE. IHIPY74FIASTEP 36 0 1 2 3 0 8 6 700 1 12 7ftI DENT* IPEIA♦INSERT. IPEI. S3

PEMAPK 8PEMAPK 8 CORRECTION. INSERT MISSING CONECT RECORDS. 83-JAN-77

♦

iNSEPT. IPEI. 1848CONECT 671 164 670

♦

INSERT. IRE 1 . 134 iCONECT 1439 332 1198♦DELETE. IPEI. I342

MASTER

47 8 0 0 18 IB 5 9 1787 2 4 18♦IDENT. IADHA

♦

iNSEPT. IADH.S7PEMAPK 5REMARK 5 rOPPEfTION. MOVE THE HET CAPDS TO THEIR PROPER POSITION.REMARK 5 ALSO CORRECT THE SHIFT FOP __ IN REMARK 4. 28-MAR-77.♦DELETE. IADH.S7

REMAP! 4 0.0 0.0 -1.8 30.85♦DELETE- 1ADH.53. 60i INSEPT. IADH.B9HET 2NI 1 1 IATALYTIC ZINCfII) lONHET 2N2 2 1 SECOND Z INC■ I I ) lONHET APP 4 35 ADP-P IEOSE ' PSEUDO COFACTOP )♦DELETE. IADH.3OI4MASTER S2 0 3 10 22 17 0 b 2822 1 45 29

♦IDENT. ICACA♦INSERT. ICAC.S3REMARK 8REMARK 8 CORRECTION. FIX MASTER RECORD TO SHOU CORRECT NUKBER OFREMARK 8 FTNOTE RECORDS. 28-MAR-77.♦DELETE. ICAC.2IB3MASTER 43 10 1 8 10 10 0 6 2859 8 4 28

♦IDENT.2CHAA♦INSERT. 2CHA. BBREI~WRK 7REMARK 7 CORRECTION. FIX SOME CONECT RECORDS THAT UERE IN ERROR.REMARK 7 28-MAR-77.♦DELETE. 2CHA. I93I. I93BCONECT 6 5 893CONECT 382 301 418CONECT 418 302 417CONECT 893 6 892CONECT 986 985 1445CONECT 1218 1217 1334CONECT 1334 1218 1333CONECT 1383 1382 1584♦DELETE. 2CHA. I94B.I94ICONECT 1445 SB6 1444CONECT 1584 1383 1583♦DELETE. 2CHA. I9S2MASTER 73 5 1 3 14 0 0 9 1796 2 21 19

♦IDENT,

3CHAC

♦

INSERT. 3CHAB. 3REMARK 8REMARK 8 CORRECTION. ORDER THE CONNECTIVITIES FOR

SEVERAL

ATOMS TOREMARK 8 BE IN ASCENDING ORDER. 28-MAR-77.♦DELETE.3CHAA.S.6CONECT 418 382 417CONECT 893 6 892♦DELETE. 3CHAB.4MASTER 45 0 0 1 14 8 0 9 1733 2 18 19

♦IDENT.ICYTA♦DELETE. ICYT.49.S2

_REMARK 6 OF THE OXIDIZED INNER MOLECULE IS GIVEN IN THE MTRIXREMARK 6 RECORDS BELOU.♦INSERT. ICYT.SSREMHRK 8REMARK 8 CORRECTION. REMOVE NON-CRYSTALLOGRAPH IC TRANSFORMATION FROMREMARK 8 REMARK 6 AND INSERT IT AS MTRIX 1 TRANSFORMATION BELOU.REMARK B 28-MAR-77 .♦INSERT. ICYT.9BMTRIX] I .418450 .907990 .021520 -50.254888MTRIX2 1 ..08170 -.041860 .002880 -17.993880MTRIX3 1 .011628 .018340 -.993760 34.745000♦DELETE. ICYT.IBBBMASTER 46 0 0 10 0 IB 0 9 1692 2 95 16

♦IDENT,

IDHBA

♦

INSERT. 1DH8.38REMARK 7REMARK 7 COPPECTION. FIX MASTER RECORD TO SHOU CORRECT NUrBER OFREMARK 7 FTNOTE RECORDS. 28-MAR-77."DELETE. IDHB.24BB1-ttSTER 35 7 2 16 0 8 0 9 2289 2 92 23

♦IDENT. IFXNA♦INSERT. IFXN.3S

REMARK 6RErrtRK 6 CORRECTION. USE

♦

INSTEAD OF SPECIAL CHARACTER -PRIME-REt-WRK 6 FOR ATOM NAMES IN THE RIBITOL PORTION OF THE FMN.REMARK 6 28-MAR-77.

♦

DELETE. ITXN. 1 163. 1171 .«____.HETATM 1093 Cl* FMN 1 30.915 -.788 13.113 1.80 0.00HETATM 1834 C2* FMN I 31.136 .658 12.625 1.00 9.60HETATM 1095 02

♦

FMN 1 31.852 1.598 13.431 1.00 0.00HETATM

1Q96

C3* FMN 1 29.744 1.196 12.314 1.00 8.08HETATM 1097 03+ FMN 1 29.398 .824 10.978 1.00 0.00HETATM 1038 C4=* FMN 1 29.b

r

".| 2.711 12.448 1.00 9.00HETATM 1A93 o_* FiVJ 1 28.280 3.126 12.443 1.00 0.00HETATM 1 100 Cs* FMN I 30.373 3.323 11.246 1.00 0.00HETATM 1101 05+ FMN 1 31.104 4.500 11.530 1.00 0.00♦DELETE. IFXN.I2O7MASTER 23 0 I 4 5 7 0 6 1 104 1 3 1 11

PROTEIN DATA BANK NEWSLETTER, No. 4 -6-

Several new Data Bank services are planned, to start during the nextsix months. These Include distribution of "model-builder's kits," to consistof compact hard-copy listings of atomic coordinates and torsion angles,intended as an aid in construction of models from standardized parts. Inaddition to these kits, we soon hope to have available for distributioncomputer programs for production of Ramachandran and diagonal plots. Theseprograms will be written in simple standard FORTRAN and will operate directlyon the atomic coordinate entries as distributed.

Currently, the majority of our budget is supplied by a grant toBrookhaven from the U.S. National Science Foundation, and we have receivedadditional support from the National Institutes of Health. These funds aregratefully acknowledged. We also appreciate very much the support of ourusers; through distribution charges paid by you, we are now recovering someof our costs. Comments and suggestions on how service might be improvedare always welcome. We want to thank all those who returned our recentquestionnaire and hope to hear from more of you in the future.

ADDRESSES NAMES:

Brookhaven National LaboratoryChemistry Department

F.C. Bernstein (tele. 516-345-4382)T.F. Koetzle (tele. 516-345-4384)G.J.B. Williams (tele. 516-345-4383)Upton, New York 11973, USA

Department of ChemistryFaculty of Science

M. Tasumi

The University of TokyoBunkyo-ku, Tokyo, Japan

University Chemical LaboratoryLens field Road

0. Kennard

Cambridge CB2 IEW, England

PROTEIN DATA BANK REQUEST

Name:

Adress

Telephone

Send the following information (please check):

( ) all current coordinate entries( ) data entries listed below

( ) description of file record formats

I am supplying a NEW 2400' reel of magnetic tape which I would like written asfollows :

( ) 7 track( ) 9 track

( ) 556 bpi ( ) BCD( ) 800 bpi ( ) ASCII( ) 1600 bpi ( ) EBCDIC

( ) Unlabelled (preferred)( ) Labelled - user's label

retained.

Tape copies of the file are normally blocked since otherwise the entirecontents will not fit on a 2400' reel of tape. Indicate the maximum block sizeallowed if blocks of 5120 characters (bytes) cannot be handled,

To avoid delays, send all correspondence to the address given on the reverseside of this form.

A purchase order ( ) /check ( ) is enclosed ( )/sent separately ( ). Thecharge is $34.30 per request or $47.00 if Brookhaven is to supply a tape.

Parameter sets requested (by code name please) :

It is expected that the Protein Data Bank be acknowledged in publications whichresult from use of the Bank's services. We would appreciate receiving reprintsof any such publications.

— —w

Protein Data BankChemistry DepartmentBrookhaven National LaboratoryUpton, New York 11973

Attn: Ms. F. C. Bernstein