Header list of 1med.pdb file
Complete list - 29 20 Bytes
HEADER AMINOACYL-TRNA SYNTHASE 09-NOV-92 1MED
TITLE METHIONYL-TRNA SYNTHETASE ZINC BINDING DOMAIN. 3D STRUCTURE AND
TITLE 2 HOMOLOGY WITH RUBREDOXIN AND GAG RETROVIRAL PROTEINS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: METHIONYL-TRNA SYNTHETASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 6.1.1.10;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 GENE: GAG;
SOURCE 5 EXPRESSION_SYSTEM_GENE: GAG
KEYWDS AMINOACYL-TRNA SYNTHASE
EXPDTA SOLUTION NMR
NUMMDL 11
AUTHOR D.FOURMY,F.DARDEL
REVDAT 6 29-NOV-17 1MED 1 REMARK HELIX
REVDAT 5 24-FEB-09 1MED 1 VERSN
REVDAT 4 01-APR-03 1MED 1 JRNL
REVDAT 3 15-JAN-95 1MED 1 COMPND
REVDAT 2 31-JAN-94 1MED 3 FTNOTE ATOM
REVDAT 1 31-OCT-93 1MED 0
JRNL AUTH D.FOURMY,F.DARDEL,S.BLANQUET
JRNL TITL METHIONYL-TRNA SYNTHETASE ZINC BINDING DOMAIN.
JRNL TITL 2 THREE-DIMENSIONAL STRUCTURE AND HOMOLOGY WITH RUBREDOXIN AND
JRNL TITL 3 GAG RETROVIRAL PROTEINS.
JRNL REF J.MOL.BIOL. V. 231 1078 1993
JRNL REFN ISSN 0022-2836
JRNL PMID 8515466
JRNL DOI 10.1006/JMBI.1993.1353
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH D.FOURMY,T.MEINNEL,Y.MECHULAM,S.BLANQUET
REMARK 1 TITL MAPPING OF THE ZINC BINDING DOMAIN OF ESCHERICHIA COLI
REMARK 1 TITL 2 METHIONYL-TRNA SYNTHETASE
REMARK 1 REF J.MOL.BIOL. V. 231 1068 1993
REMARK 1 REFN ISSN 0022-2836
REMARK 1 REFERENCE 2
REMARK 1 AUTH S.BRUNIE,C.ZELWER,J.-L.RISLER
REMARK 1 TITL CRYSTALLOGRAPHIC STUDY AT 2.5 ANGSTROMS RESOLUTION OF THE
REMARK 1 TITL 2 INTERACTION OF METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA
REMARK 1 TITL 3 COLI WITH ATP
REMARK 1 REF J.MOL.BIOL. V. 216 411 1990
REMARK 1 REFN ISSN 0022-2836
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1MED COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000174971.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 1 PHE A 5 CB - CG - CD2 ANGL. DEV. = 8.7 DEGREES
REMARK 500 1 PHE A 5 CB - CG - CD1 ANGL. DEV. = -10.5 DEGREES
REMARK 500 1 PHE A 5 N - CA - C ANGL. DEV. = -17.0 DEGREES
REMARK 500 1 LYS A 14 N - CA - CB ANGL. DEV. = -12.1 DEGREES
REMARK 500 2 PHE A 5 CB - CG - CD2 ANGL. DEV. = 5.8 DEGREES
REMARK 500 2 PHE A 5 CB - CG - CD1 ANGL. DEV. = -8.1 DEGREES
REMARK 500 2 VAL A 6 CA - C - N ANGL. DEV. = -14.7 DEGREES
REMARK 500 2 LYS A 7 N - CA - C ANGL. DEV. = -20.4 DEGREES
REMARK 500 2 LYS A 14 N - CA - CB ANGL. DEV. = -10.9 DEGREES
REMARK 500 2 ALA A 28 N - CA - C ANGL. DEV. = 21.4 DEGREES
REMARK 500 3 PHE A 5 CB - CG - CD2 ANGL. DEV. = -10.1 DEGREES
REMARK 500 3 PHE A 5 CB - CG - CD1 ANGL. DEV. = 8.8 DEGREES
REMARK 500 3 CYS A 10 CA - CB - SG ANGL. DEV. = 12.7 DEGREES
REMARK 500 3 LYS A 14 N - CA - CB ANGL. DEV. = -12.6 DEGREES
REMARK 500 3 CYS A 23 CA - CB - SG ANGL. DEV. = 10.2 DEGREES
REMARK 500 4 PHE A 5 CB - CG - CD2 ANGL. DEV. = -12.3 DEGREES
REMARK 500 4 PHE A 5 CB - CG - CD1 ANGL. DEV. = 11.6 DEGREES
REMARK 500 4 LYS A 14 N - CA - CB ANGL. DEV. = -14.1 DEGREES
REMARK 500 4 CYS A 26 CA - CB - SG ANGL. DEV. = 8.5 DEGREES
REMARK 500 4 ALA A 28 N - CA - C ANGL. DEV. = 21.1 DEGREES
REMARK 500 5 PHE A 5 CB - CG - CD2 ANGL. DEV. = -9.8 DEGREES
REMARK 500 5 PHE A 5 CB - CG - CD1 ANGL. DEV. = 7.7 DEGREES
REMARK 500 5 LYS A 14 N - CA - CB ANGL. DEV. = -11.4 DEGREES
REMARK 500 6 PHE A 5 CB - CG - CD2 ANGL. DEV. = -10.8 DEGREES
REMARK 500 6 PHE A 5 CB - CG - CD1 ANGL. DEV. = 8.0 DEGREES
REMARK 500 6 LYS A 14 N - CA - CB ANGL. DEV. = -14.6 DEGREES
REMARK 500 7 PHE A 5 CB - CG - CD2 ANGL. DEV. = -7.8 DEGREES
REMARK 500 7 PHE A 5 CB - CG - CD1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 7 LYS A 14 N - CA - CB ANGL. DEV. = -13.9 DEGREES
REMARK 500 8 VAL A 6 CA - CB - CG1 ANGL. DEV. = -9.2 DEGREES
REMARK 500 8 VAL A 6 CA - C - N ANGL. DEV. = -15.5 DEGREES
REMARK 500 8 LYS A 7 N - CA - C ANGL. DEV. = -16.2 DEGREES
REMARK 500 8 LYS A 14 N - CA - CB ANGL. DEV. = -13.0 DEGREES
REMARK 500 8 CYS A 26 CA - CB - SG ANGL. DEV. = 7.8 DEGREES
REMARK 500 9 PHE A 5 CA - CB - CG ANGL. DEV. = -17.2 DEGREES
REMARK 500 9 PHE A 5 CB - CG - CD2 ANGL. DEV. = -9.8 DEGREES
REMARK 500 9 PHE A 5 CB - CG - CD1 ANGL. DEV. = 7.3 DEGREES
REMARK 500 9 LYS A 14 N - CA - CB ANGL. DEV. = -13.5 DEGREES
REMARK 500 9 CYS A 26 CA - CB - SG ANGL. DEV. = 6.9 DEGREES
REMARK 500 10 PHE A 5 CB - CG - CD2 ANGL. DEV. = -9.4 DEGREES
REMARK 500 10 PHE A 5 CB - CG - CD1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 10 CYS A 13 CA - CB - SG ANGL. DEV. = 7.2 DEGREES
REMARK 500 10 LYS A 14 N - CA - CB ANGL. DEV. = -12.1 DEGREES
REMARK 500 11 PHE A 5 CB - CG - CD2 ANGL. DEV. = -9.4 DEGREES
REMARK 500 11 PHE A 5 CB - CG - CD1 ANGL. DEV. = 6.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ARG A 4 -64.13 -21.08
REMARK 500 1 LYS A 7 64.09 3.79
REMARK 500 1 LYS A 14 76.09 49.82
REMARK 500 1 PRO A 16 -41.28 -21.96
REMARK 500 1 GLN A 18 73.77 -100.63
REMARK 500 1 ASN A 22 99.06 -8.99
REMARK 500 1 CYS A 23 107.71 -26.18
REMARK 500 2 SER A 2 68.25 -112.90
REMARK 500 2 ASP A 3 69.51 -114.70
REMARK 500 2 LYS A 7 40.09 -140.26
REMARK 500 2 LYS A 14 76.57 57.30
REMARK 500 2 PRO A 16 -36.57 -27.44
REMARK 500 2 ASN A 22 69.23 1.10
REMARK 500 2 CYS A 23 127.73 -1.84
REMARK 500 2 VAL A 25 -59.38 -124.28
REMARK 500 3 ARG A 4 -58.29 96.00
REMARK 500 3 LYS A 7 62.01 25.45
REMARK 500 3 CYS A 10 91.60 -49.38
REMARK 500 3 LYS A 14 80.34 -44.12
REMARK 500 3 ASP A 17 86.80 -150.13
REMARK 500 3 ASP A 21 39.76 -92.31
REMARK 500 3 ASN A 22 65.74 2.42
REMARK 500 3 CYS A 23 52.24 26.18
REMARK 500 3 CYS A 26 -52.68 -123.77
REMARK 500 4 LYS A 7 71.50 98.03
REMARK 500 4 LYS A 14 77.19 6.52
REMARK 500 4 PRO A 16 -40.48 -15.45
REMARK 500 4 GLN A 18 65.96 -100.94
REMARK 500 4 ASN A 22 124.64 64.94
REMARK 500 4 CYS A 23 102.26 -18.43
REMARK 500 5 ARG A 4 -63.22 90.79
REMARK 500 5 PHE A 5 -149.15 -132.43
REMARK 500 5 LYS A 7 89.53 85.17
REMARK 500 5 LYS A 14 87.83 52.57
REMARK 500 5 PRO A 16 -56.59 -10.05
REMARK 500 5 GLN A 18 70.72 -102.31
REMARK 500 5 ASN A 22 82.62 -8.69
REMARK 500 5 CYS A 23 100.41 -3.19
REMARK 500 5 GLU A 24 41.06 -101.46
REMARK 500 5 VAL A 25 -58.17 -120.21
REMARK 500 6 ARG A 4 -66.77 -25.96
REMARK 500 6 LYS A 7 86.01 101.54
REMARK 500 6 LYS A 14 75.17 21.73
REMARK 500 6 PRO A 16 -49.54 -14.72
REMARK 500 6 ASN A 22 74.92 12.21
REMARK 500 6 CYS A 23 91.72 16.79
REMARK 500 7 SER A 2 162.93 69.33
REMARK 500 7 ARG A 4 -60.79 -24.16
REMARK 500 7 LYS A 7 72.47 40.49
REMARK 500 7 CYS A 10 96.39 -50.65
REMARK 500
REMARK 500 THIS ENTRY HAS 87 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 CYS A 10 PRO A 11 1 -138.35
REMARK 500 SER A 15 PRO A 16 1 -129.37
REMARK 500 CYS A 10 PRO A 11 2 -133.69
REMARK 500 SER A 15 PRO A 16 2 -126.85
REMARK 500 CYS A 10 PRO A 11 4 -147.34
REMARK 500 SER A 15 PRO A 16 4 -136.59
REMARK 500 CYS A 10 PRO A 11 5 -132.18
REMARK 500 CYS A 10 PRO A 11 6 -143.86
REMARK 500 SER A 15 PRO A 16 6 -146.12
REMARK 500 CYS A 10 PRO A 11 8 -148.67
REMARK 500 SER A 15 PRO A 16 8 -145.34
REMARK 500 CYS A 10 PRO A 11 9 -144.95
REMARK 500 SER A 15 PRO A 16 9 -125.87
REMARK 500 CYS A 10 PRO A 11 10 -138.47
REMARK 500 SER A 15 PRO A 16 10 -139.22
REMARK 500 CYS A 10 PRO A 11 11 -147.33
REMARK 500 SER A 15 PRO A 16 11 -124.00
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 ARG A 4 0.27 SIDE CHAIN
REMARK 500 2 ARG A 4 0.17 SIDE CHAIN
REMARK 500 3 ARG A 4 0.21 SIDE CHAIN
REMARK 500 4 ARG A 4 0.19 SIDE CHAIN
REMARK 500 5 ARG A 4 0.32 SIDE CHAIN
REMARK 500 6 ARG A 4 0.20 SIDE CHAIN
REMARK 500 7 ARG A 4 0.29 SIDE CHAIN
REMARK 500 8 ARG A 4 0.30 SIDE CHAIN
REMARK 500 9 ARG A 4 0.31 SIDE CHAIN
REMARK 500 10 ARG A 4 0.31 SIDE CHAIN
REMARK 500 11 ARG A 4 0.32 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 29 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 10 SG
REMARK 620 2 CYS A 26 SG 109.4
REMARK 620 3 CYS A 23 SG 104.8 110.9
REMARK 620 4 CYS A 13 SG 109.1 113.1 109.3
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ZNC
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: NULL
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 29
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1MEA RELATED DB: PDB
DBREF 1MED A 3 28 UNP P00959 SYM_ECOLI 138 163
SEQRES 1 A 28 GLY SER ASP ARG PHE VAL LYS GLY THR CYS PRO LYS CYS
SEQRES 2 A 28 LYS SER PRO ASP GLN TYR GLY ASP ASN CYS GLU VAL CYS
SEQRES 3 A 28 GLY ALA
HET ZN A 29 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
LINK ZN ZN A 29 SG CYS A 10 1555 1555 2.29
LINK ZN ZN A 29 SG CYS A 26 1555 1555 2.30
LINK ZN ZN A 29 SG CYS A 23 1555 1555 2.18
LINK ZN ZN A 29 SG CYS A 13 1555 1555 2.30
SITE 1 ZNC 4 CYS A 10 CYS A 13 CYS A 23 CYS A 26
SITE 1 AC1 4 CYS A 10 CYS A 13 CYS A 23 CYS A 26
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - 29 20 Bytes