PDB Short entry for 1MED 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