April 19sP^CEI\/£qTHXPROTEIN DATA BANKNumber 16NEWSLETTER *Pft^_

The Protein Data Bank recently has added atomic coordinates for scfip^ PCinrpolydeoxyribonucleotide structures to our holdings, as indicated in Table 3.Already a number of requests for the data have been received. We are very pleasedto be able to make these DNA structures available and are looking forward toreceiving others in the future.

We presently have 1100 names on the Newsletter mailing list, and risingpostal rates make mailings increasingly costly. Therefore, we would appreciateyour returning the form below if you wish to remain on our mailing list. The formcan also be used to give corrections or additional names who are interested in theData Bank's services.

In early April, Brookhaven will change its telephone exchange from 345 to282. Extensions will remain the same as before. Please note our new numbers aslisted below.

It is expected that the Protein Data Bank be acknowledged in publicationswhich result from work making use of the Bank's services. In citing the ProteinData Bank in print, we suggest that a reference be included to F. C. Bernstein,T. F. Koetzle, G. J. B. Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers,0. Kennard, T. Shimanouchi, and M. Tasumi, Jwould appreciate receiving reprints.

Address of CenterArea

The Americas Protein Data BankChemistry DepartmentBrookhaven National LaboratoryUpton, New York 11973 USA

University Chemical LaboratoryLensfield Road

Europe andWorldwide

Cambridge CB2 IEW, England

CSIRO Div. of Chemical PhysicsP. 0. Box 160

Australia

Clayton, Victoria 3168 Australia

Institute for Protein ResearchOsaka University

Japan

5311, Yamada-Kami, SuitaOsaka, Japan

Please ( ) keep my name on the mailing list( ) delete my name from the mailing list( ) add my name to the mailing list

Name

Mol. Biol. 112, 535-42 (1977). We

Name

E. Abola 516-282-4383F. C. Bernstein 516-282-4382T. F. Koetzle 516-282-4384516-282-4384

Ms. F. C. BernsteinChemistry DeptBrookhaven NationalLaboratory

Upton, NY 11973 USAAddress

Telephone

Number 16Protein Data Bank NewsletterApril 1981Page 2

TABLE I. PROTEIN DA IA

HANK,

INFORMATION AVAILABLE ON MAGNETIC TAPE

01-APR-BI

l;l

ITEM NO.TAPES AVAILABILITY800 1600 US UK JA AUS

DATAPRTP ALL CURRENT PROGRAMS. BIBLIOGRAPHIC ENTRIES, 8 I X X X XCOORDINATE ENTRIES ITABLES 3. 4. 61

NONSTDTP ALL STRUCTURE FACTOR HOLDINGS (TABLE 51 2 1 XXXBENDERTP PARAMETERS FOR BENT-WIRE MODELS I I XBLDKITTP MODEL BUILDER -S KIT PLEASE

INQUIRE

AT US CENTERCONECTTP CONNECTIVITY SPECIFICATIONS FOR ALL ATOMS 8 ] XDGPLOTTP DIAGONAL

PLOTS

(LINE PRINTER) 1 1 X1 1 XDIHDRLTP COMPLETE TORSION ANGLES 8 1 X

DSTNCETP

CONNECTIVITY SPECIFICATIONS WiTH DISTANCES 2 1 XFISIPLTP PHI/PSI PLOTS (LINE PRINTERI 1 1 X1 1 XPHIPSITP LISTS OF PHI /PSI /OMEGA VALUES 1 1 X

NEW OR REPLACEMENT ENTRY SINCE JAN-81 NEWSLETTER

TABLE _ PROTEIN DATA BANK.

INFORMATION

AVAILABLE ON MICROFICHE

0 1-APR-BI

AVAILABILITYUS UK JA AUSCODE ITEM

DATAPRFI ALL CURRENT

COORDINATEENTRIES

AND PROGRAMS 'TABLES 3.11 < J <NONSTDFI ALL STRUCTURE FACTOR HOLDINGS I TABLE 51 X X X

CORRO7FI

-LIST OF

CORRECTIONS

NO. 7 I

JUL/BO

. JAN/B I 1

BENDERFI PARAMETERS TOR BENT-WIRE MODELS ,___,_ HE AT US

CENTER

BLDKITFI MODEL BUILDER _ KIT PLEASE

INQUIRE

AT US CENILK

CONECTFI

CONNECTIVITY

SPECIFICATIONS

FOR ALL ATOMSLUNLL I h I

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NEW OR REPLACEMENT ENTRY

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JAN-8] NEWSLETTER

jTABLE 3. PROTEIN DATA BANK. ATOMIC COORDINATE HOLDINGS V 1APR-8J l-J h3

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9/79

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1J

AVAILABLE PROGPAMSPROTEIN DATA BANKTABLE

01-APP-8I

REV DATE'SLIPPOR TED

AUTHOR IS'NAME PURPOSE

BENDER PARAMETERS FOR BENT-WIRE MODELS G. WILLIAMS 1 79 YESBLDKIT MODEL BUILDER'S KIT E . ABOLA 7/BO YESCHIRAL CHECK

CHIRALITY

E ABOLACONECT GENERATE Fun CONNECT.

■.

Ii . F BERNSTEINCONTCT INTERMOLECULAR

CONTACTS

_ ANDREWS 10. ""9 NCDGPLOT DIAGONAL PLOTS ON PRINTER E . SWANSON

,F

.BERNSTE I N 3 79 fESDIHDRL COMPLETE TORSION ANGLES E ABOLA 3/80 _S

DSTNCE CALC DISTANCES FROM CONECT RECORDS F.BERNSTEIN I 79 itFISIPL PHI PSI PLOTS ON PRINTER F BERNSTEIN 5/79 YESNAMOD BALL-AND-STICK MODEL DISPLAY . BEPPU 1 1

7

8 NOPHIPS! MAIN-CHAIN TORSION ANGLES ANDREWS

,WI

LL I AMS

.BERNSTE

I NSTEREO EXTRACT X.Y.Z FROM STEREO DIAGRAMS M ROSSMANN 6/79 NOTAPDIR PRINT DIRECTORY OF TAPE CONTENTS H.BERNSTEIN.) BERNSTEIN 12/79 (EC

TORSRU COMPLETE TORSION ANGLES . _EKE in

7S

VALIDATION OF MASTER RECORD L ANDREWS. F . BERNSTE 1 1. - <8 /E

NEW OR REPLACEMENT ENTRY SINCE JAN-6I

NEWSLtTTEP

SUPPORTED PROGRAMS ARE THOSE FOR WHICH STAFF OF THE PROTEIN DATA BANK WILLPROVIDE CORRECTIONS FOR DEMONSTRATED ERRORS.

TABLE 5. PROTEIN DATA BANK. STRUCTURE FACTOR

HOLDINGS

01-APR-BI

DATEIDENTCODE CODEDEPOSITORMOLECULE

PIACTSF ACTINIDIN E.BAKER 7/77 SFCHYMOF ALPHA-CHYMOTRYPSIN I TOSYL I D.BLOW 4/73 SFRCARPO4 CALCIUM-BINDING PARVALBUMIN R.KRETSINGER 2/ '4 SFRCARPOS CALCIUM-BINDING PARVALBUMIN R.KRETSINGER 2/74 SFR2BSCSF CYTOCHROME 85 F.S.MATHEWS _ 12/77 SFR3CYTSF CYTOCHROME C

IALBACORE.

OXIDIZED! T . TAKANO ,R -DI CKERSON 7 8C 5

r

R4CYTSF CYTOCHROME C IALBACORE. REDUCED' T TAKANO

,R

. DI CKERSON 7/80 SFRCYCSSO! CYTOCHROME C550 R.TIMKOVICH 4/76 SFRTSICSF CYTOCHROME C5 51 P DICKERSON 8/78 SFRIZNASF -DNAIZi

,CGCG,

HIGH-SALT. SYNTHET IC ' H.DREW. R. DICKERSON I'BI SFRGPDO4 GLYCERALDEHYDE-3-P-DEHYDROGENASEILOBSTRIM,ROSSMANN B 75 SFR2GPDSF APO-GLYCERALDEHYDE-3-P-DEHYDROGENASE M . ROSSMANN 12/79 SFR2MHBSF HEMOGLOBIN (HORSE.

AQUO

MET ANC : LADNER.HE I DNER.PERUT7 6/80 SFRIFDHSF HEMOGLOBIN (HUMAN. FETAL. DEOXY) J.FRIER 6/80 Si-RHUMOEHO2 HEMOGLOBIN IHUMAN .DEOXY ) M. PERUTZ

.G

.FERMILAMPRYI HEMOGLOBIN (LAMPpg HENDRI CKSON

.LOVE

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DEHYDROGENASE

'S-LAC' NAD IPIGI U.GRAU .M. ROSSMANN l/Bl SFRMETMYSFI MYOGLOBIN ISPERM WHALE . MET) T . TAKANO 6/76 SFRDEMYSF I MYOGLOBIN i SPERM WHALE. DEOXY) T TAKANO 6 76 SF

R4TNASF TRANSFER RNA [YEAST. PHE A . JACK . J. LADNER. A.KLUG 6/BO SF

NEW OR REPLACEMENT ENTRY SiNCE JAN-BI NEWSLETTER

CODES

SF STRUCTURE FACTORS

TABLE 6. PROTEIN DATA BANK. BIBLIOGRAPHIC ENTRIES

ACID

PROTEINASE

(ENDCTHIA PARASITICA!APOFERRITIN 'HORSE!

OEAPOAF IOMAAOCTSOCTXOCNIOCNBOCYPOCCYDCY305C1OESZOETUOEBXOFDI

MITOCHONDRIAL ASPARTATE AMINOTRANSFERASECITRATE SYNTHASE IPIGIALPHA COBRATOXINCONCANAVALIN A IDEMETALL I ZEDICONCANAVALIN A ( DEMET ALL I ZED )

CYTOCHROME C PEROXIDASE ISACCHAROMYCES CEREVISIAE'CYTOCHROME C- (RHODOSP IR ILLUM MOL I SCHI ANUMICYTOCHROME C 3IDESULFOV I BRIO DESULFURICANS NORWAY ICYTOCHROME C555 'CHLOROBIUM THIOSULFATOPHILUM)ELASTASE COMPLEX iPIGI

ELONGATION

FACTOR TU COMPLEX lE. COLI!ERABUTOXIN BFERREDOXIN

lAZOTOBALTER

VINLANDI!)FLAVODOXIN (DESULFOVIBR 10 VULGARIS)FLAVODOXIN (REDUCED.

CLOSTRIDIUM

MP!GLUTATHIONE PEROXIDASE I80V I NE )

OFX?OGPIOGDIOHBGOPHHOAUIOROYOMCPOFB4OFC2OFCI01GIOIG2OIN2OGFI

QGF

2OLZIOLZ2OLZSOCTFOMBS3MBMOMB3OMB4

OBP2OBPIOPPAOPBIORXSORSAORN3OFMTOTAIOTA2OTRIOTSIOGNSOUTGOTMVOTBV

NEW OR REPLACEMENT ENTRY SINCE JAN-81 NEWSLETTER

01-APR-81

D-GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE

18/".L.US

STEAROTHERMOPHILUS)HEMOGLOBIN (GLvCERa DIBRANCHIATAP-HYOPOXYBENZOATE HYDROXYLASE IPSEUDOMONAS TLUURESCENS)IMMUNOGLOBULIN.

BENCE-JONES

FRAGMENT (KAPPA) AU

IMMUNOGLOBULIN,

BENCE -JONES FRAGMENT ( V-MONOMER. KAPPA I ROYIMMUNOGLOBULIN FAB 'KAPPAI MCP6O3IMMUNOGLOBULIN FAB (LAMBDA! KOLIMMUNOGLOBULIN FC (HUMAN! - FRAGMENT B OF PROTEIN A (STAPH AUREUS) COMPLEXI MMUNOGLOBULI N FC I HUMANIIMMUNOGLOBULIN Gl 'KAPPA) DOBIMMUNOGLOBULIN G] (LAMBDA) KOLI NSUL I N ( PCRC INEIINSULIN-LIKE GROWTH FACTOR 1 (HUMAN)INSULIN-LIKE GROWTH FACTOR II (HUMAN)LYSOZYML (HUMAN)LYSOZYME (TURKEY)LYSOZYME (HEN EGG-WHITE. NEUTRON STUDY)L7/Ll2 lE.

COLI,

C- TERMINUS IMVOGLOBIN ISPERM WHALE. CARBON MONOXIDE. NEUTRON STUDY!"YOGLOBIN ISPERM WHALE. MET. TEMPERATURE STUDIES'MYOGLOBIN (SPERM WHALE.

MET,

NEUTRON STUDY!MYOGLOBIN (SPERM WHALE. OXY IPHOSPHOFRUCTOKINASE (BACILLUS STEAROTHERMOPHIL IUS IPHOSPHOLIPASE A 8(BOVINE!PHOSPHOL I PASE A 2IPCRC I NE IPHOSPHORYLASE A (RABBIT)PHOSPHORYLASE B iRABBIT.RELAX I N I PORC I NE . MODEL )

RIBONUCLEASE

A IBOVINEIRIBONUCLEASE A IBOVINEIINITIATOR TRANSFER RNA lE.

COLI.

F/MET)"TRANSFER RNA (YEAST,

ASP.

A F^RMI■TRANSFER RNA (YEAST.

ASP,

B FORM)TRANSFER RNA 'YEAST . PHE)TYROSYL TRANSFER RNA SYNTHETASE (BACILLUS STEAROTHERMOPHILUS)

GENE 5 DNA-UMWINDING PROTEIN lE. COLI!UTEROGLOBIN [RABBIT!vIRUS PROTEIN DISK (TOBACCO MOSAIC!VIRUS (TOMATO BUSHY STUNT.

r. )-.. l-i0.

O

CO

rr_....-r23

CD

.H1(Drrrrto.

RRUBYOP RUBREDOXIN L.JENSEN

3/74

=F

> SST_ .* s.. ■ C.

h-_3 r- 1

00 0"i

Protein Data Bank Newsletter Number 16

2. Tape format desired (all tapes are unlabelled)

( ) 9 track, 1600 cpi, EBCDIC( ) 9 track, 800 cpi, EBCDIC( ) 9 track, 1600 cpi, ASCII( ) 9 track, 800 cpi, ASCII( ) 7 track, 800 cpi, BCD

Only the first two formats are normally prepared at Cambridge; pleaseinquire for availabilityof other formats.

All tapes are distributed in blocked form with fixed record length andblock size. Brookhaven normally uses a block size close to, but lessthan, 5120 characters. Please indicate here any difficulties this mightcause .

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4. Please send the following magnetic tape items (from Table 1). Each1-tape item costs $96 (^-45); each 2-tape item costs $116 (^ 53).

Item Number of Tapes Cost

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Number 16Protein Data Bank NewsletterApril 1981Page 6

items (from Table 2). Each5. Please send the following microfichemicrofiche item costs $81 (^36 from Cambridge). Correction fiche arefree.

CostItem

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Protein Data Bank

Please return to

Dr. S. BellardMs. F. C. BernsteinChemistry Department

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Upton, New York 11973 USA Cambridge CB2 IEW, England