£q - stanford universitygw128wm4806/gw128wm4806.pdf · number 16 protein data bank newsletter...
TRANSCRIPT
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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S<Lbiriv.ili.h. .v. -_- ._
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WITH DISTANCES
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1
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-
■ ■ ■
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NEW OR REPLACEMENT ENTRY
SINCE
JAN-8] NEWSLETTER
jTABLE 3. PROTEIN DATA BANK. ATOMIC COORDINATE HOLDINGS V 1APR-8J l-J h3
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GEMANN
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'
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12/77
R ,SRX THIOREDOX I N lE . COL I.OX ID I ZED ' Bgo . SODERBERG 5/76 A?X IN .CLOSTRIDIUM MP. SEMI
QUI
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AQUO
METI R . LADNER , HE I DNER.PERUTZ B"P jFT p TRYPSIN (DIP
INHIBITED,
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DEOXY,
M . PERUTZ .G. FERMI - -. , Tp , TRYPS I NOGEN/TRYPS I N INHIBI TOR/ ILE-VAL W . BODE . P . SCHWAGER .R . HUBER
3/79
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HEMOGLOBIN.
HUMAN.CARBONMONOXY . NRG REFNDI_BALDWIN 879 ,TGB TRYPSINOGEN (WITH CA FROM PEG! BODE .FEHLHAMMER. HUBER 3/79 jtsIFDH HEMOGLOBIN (HUMAN. FETAL. DEOXY) J.FRIER 3 76 T TRYPSINOGEN A.KOSS I AKOFF .B STROUD
9/79
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MIHKG HEXOKINASE A -
GLUCOSECOMPLEX
.TEAST i W.BENNETT JR..T.bTEITZ 12 BOSYHX HEXOKINASE .YEAST) FORM BUI STE I TZ .ANDERSON, STENKAMP
3/78
1 . NEW 0H PEP' ACEMENT ENTRY S I NCE JAN-B1 NEWSLETTERIHIP HIGH POTENTI\L IRON PROTEIN J.KRAUT -
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-
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SALT,
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HYALURONICACID
INA
SALT. 2-FOLD
HELIX!
S.ARNOTT
5 78 BLANK STANDARD ENTR» AVAILABLE FOR DISTRIBUTION4HYA HYALURONIC ACID .CA SALT. 3-FOLD HEL IX ' S ARNOTT 578 A ALpHA CARBON ATOMS ONLY2FAB
IMMUNOGLOBULIN
FAB- NEW
RPOLJAK
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12/77
A fi REPLACES AN OUT-OF-DATE PARAMETER SETI INS INSULINIPORCINE.2-ZINC) G . DODSON . D . HODGK I N
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
.KARIE 5/73 SFRLDHO6 LACTATE DEHYDROGENASE M .ROSSMANN B/75 SFRLDHO7 LACTATE DEHYDROGENASE NAD'PrRUVATE M .ROSSMANN B/75 SFRSLDHSF -LACTATE
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
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Number 16Protein Data Bank NewsletterApril 1981Page 6
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