HEADER AMINOACYL-TRNA SYNTHETASE 09-JUN-95 1KRS TITLE SOLUTION STRUCTURE OF THE ANTICODON BINDING DOMAIN OF ESCHERICHIA COLI TITLE 2 LYSYL-TRNA SYNTHETASE AND STUDIES OF ITS INTERACTIONS WITH TRNA-LYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSYL-TRNA SYNTHETASE (PRODUCT OF LYSS GENE); COMPND 3 CHAIN: A; COMPND 4 EC: 6.1.1.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: JM101TR; SOURCE 5 GENE: LYSS CODONS 40 - 149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: LAC; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRC-ND; SOURCE 10 EXPRESSION_SYSTEM_GENE: LYSS CODONS 40 - 149; SOURCE 11 OTHER_DETAILS: PTRC99A (IPTG-INDUCIBLE LAC PROMOTER) KEYWDS AMINOACYL-TRNA SYNTHETASE EXPDTA SOLUTION NMR AUTHOR S.COMMANS,F.DARDEL REVDAT 3 23-FEB-22 1KRS 1 REMARK SEQADV REVDAT 2 24-FEB-09 1KRS 1 VERSN REVDAT 1 15-SEP-95 1KRS 0 JRNL AUTH S.COMMANS,P.PLATEAU,S.BLANQUET,F.DARDEL JRNL TITL SOLUTION STRUCTURE OF THE ANTICODON-BINDING DOMAIN OF JRNL TITL 2 ESCHERICHIA COLI LYSYL-TRNA SYNTHETASE AND STUDIES OF ITS JRNL TITL 3 INTERACTION WITH TRNA(LYS). JRNL REF J.MOL.BIOL. V. 253 100 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7473706 JRNL DOI 10.1006/JMBI.1995.0539 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.LEVEQUE,P.PLATEAU,P.DESSEN,S.BLANQUET REMARK 1 TITL HOMOLOGY OF LYSS AND LYSU, THE TWO ESCHERICHIA COLI GENES REMARK 1 TITL 2 ENCODING DISTINCT LYSYL-TRNA SYNTHETASE SPECIES REMARK 1 REF NUCLEIC ACIDS RES. V. 18 305 1990 REMARK 1 REFN ISSN 0305-1048 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KRS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174484. 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 : 1 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 ALA A 30 REMARK 465 GLU A 31 REMARK 465 GLN A 32 REMARK 465 GLY A 33 REMARK 465 ILE A 34 REMARK 465 ALA A 35 REMARK 465 PHE A 36 REMARK 465 PRO A 37 REMARK 465 ASN A 38 REMARK 465 ASP A 39 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 44 CG HIS A 44 ND1 -0.095 REMARK 500 ALA A 69 CA ALA A 69 CB -0.258 REMARK 500 ALA A 83 CA ALA A 83 CB -0.173 REMARK 500 TRP A 116 CG TRP A 116 CD2 -0.106 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 ASP A 43 N - CA - C ANGL. DEV. = -22.7 DEGREES REMARK 500 HIS A 44 CA - CB - CG ANGL. DEV. = 20.4 DEGREES REMARK 500 LEU A 49 CB - CG - CD2 ANGL. DEV. = -12.9 DEGREES REMARK 500 GLU A 59 CA - C - N ANGL. DEV. = -14.9 DEGREES REMARK 500 VAL A 68 CA - CB - CG1 ANGL. DEV. = -9.6 DEGREES REMARK 500 VAL A 68 CA - C - N ANGL. DEV. = -19.1 DEGREES REMARK 500 ALA A 69 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 ALA A 69 N - CA - C ANGL. DEV. = 21.4 DEGREES REMARK 500 ALA A 69 CA - C - N ANGL. DEV. = -18.5 DEGREES REMARK 500 THR A 76 CA - CB - CG2 ANGL. DEV. = -10.8 DEGREES REMARK 500 TYR A 98 CB - CG - CD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 TYR A 98 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ALA A 100 N - CA - CB ANGL. DEV. = -8.9 DEGREES REMARK 500 TYR A 109 N - CA - CB ANGL. DEV. = -12.3 DEGREES REMARK 500 GLU A 111 CA - CB - CG ANGL. DEV. = -19.3 DEGREES REMARK 500 GLN A 112 N - CA - CB ANGL. DEV. = -14.5 DEGREES REMARK 500 GLN A 112 N - CA - C ANGL. DEV. = -17.9 DEGREES REMARK 500 PHE A 113 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 PHE A 113 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 TRP A 116 CA - CB - CG ANGL. DEV. = -18.7 DEGREES REMARK 500 TRP A 116 CB - CG - CD2 ANGL. DEV. = 9.2 DEGREES REMARK 500 TRP A 116 CB - CG - CD1 ANGL. DEV. = -14.2 DEGREES REMARK 500 TRP A 116 CA - C - N ANGL. DEV. = -13.5 DEGREES REMARK 500 ASP A 117 CA - C - N ANGL. DEV. = -13.8 DEGREES REMARK 500 LEU A 118 CB - CG - CD2 ANGL. DEV. = -13.0 DEGREES REMARK 500 GLY A 123 N - CA - C ANGL. DEV. = -20.3 DEGREES REMARK 500 LEU A 136 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 LEU A 136 N - CA - C ANGL. DEV. = 26.4 DEGREES REMARK 500 LEU A 145 CB - CG - CD2 ANGL. DEV. = 12.5 DEGREES REMARK 500 LEU A 146 N - CA - CB ANGL. DEV. = -13.0 DEGREES REMARK 500 LEU A 146 CA - CB - CG ANGL. DEV. = -17.6 DEGREES REMARK 500 LEU A 146 CB - CG - CD2 ANGL. DEV. = 10.8 DEGREES REMARK 500 LEU A 146 CA - C - O ANGL. DEV. = 13.0 DEGREES REMARK 500 LEU A 146 CA - C - N ANGL. DEV. = -25.9 DEGREES REMARK 500 LEU A 146 O - C - N ANGL. DEV. = 12.9 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 ARG A 41 -158.72 -107.83 REMARK 500 HIS A 44 -100.17 -13.94 REMARK 500 SER A 46 89.75 98.06 REMARK 500 PHE A 53 -37.21 -38.44 REMARK 500 LYS A 56 -167.97 -121.22 REMARK 500 ASN A 65 143.37 -15.51 REMARK 500 GLU A 67 66.28 -111.00 REMARK 500 MET A 74 -149.62 -161.81 REMARK 500 MET A 75 9.90 179.19 REMARK 500 ARG A 78 51.96 -141.03 REMARK 500 ILE A 79 153.85 -47.60 REMARK 500 MET A 80 38.73 -152.09 REMARK 500 LYS A 82 -151.03 -119.95 REMARK 500 ALA A 83 114.12 -3.21 REMARK 500 VAL A 91 -60.45 -24.48 REMARK 500 PRO A 105 64.06 -69.99 REMARK 500 VAL A 108 -19.51 -47.09 REMARK 500 TYR A 109 -144.19 -74.68 REMARK 500 ASN A 110 -17.96 -40.43 REMARK 500 LEU A 118 -114.63 -28.98 REMARK 500 LYS A 130 90.77 -46.48 REMARK 500 GLU A 135 -112.42 -112.50 REMARK 500 LEU A 136 7.29 -21.12 REMARK 500 HIS A 139 77.95 -117.03 REMARK 500 THR A 141 -31.66 -132.83 REMARK 500 LEU A 146 -168.82 -78.61 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 ARG A 42 0.32 SIDE CHAIN REMARK 500 ARG A 73 0.30 SIDE CHAIN REMARK 500 ARG A 77 0.31 SIDE CHAIN REMARK 500 ARG A 78 0.30 SIDE CHAIN REMARK 500 ARG A 94 0.28 SIDE CHAIN REMARK 500 ARG A 101 0.31 SIDE CHAIN REMARK 500 ARG A 144 0.28 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KRT RELATED DB: PDB DBREF 1KRS A 30 149 UNP P0A8N3 SYK1_ECOLI 26 148 SEQADV 1KRS A UNP P0A8N3 ASN 27 DELETION SEQADV 1KRS A UNP P0A8N3 LEU 28 DELETION SEQADV 1KRS A UNP P0A8N3 ARG 29 DELETION SEQRES 1 A 120 ALA GLU GLN GLY ILE ALA PHE PRO ASN ASP PHE ARG ARG SEQRES 2 A 120 ASP HIS THR SER ASP GLN LEU HIS ALA GLU PHE ASP GLY SEQRES 3 A 120 LYS GLU ASN GLU GLU LEU GLU ALA LEU ASN ILE GLU VAL SEQRES 4 A 120 ALA VAL ALA GLY ARG MET MET THR ARG ARG ILE MET GLY SEQRES 5 A 120 LYS ALA SER PHE VAL THR LEU GLN ASP VAL GLY GLY ARG SEQRES 6 A 120 ILE GLN LEU TYR VAL ALA ARG ASP ASP LEU PRO GLU GLY SEQRES 7 A 120 VAL TYR ASN GLU GLN PHE LYS LYS TRP ASP LEU GLY ASP SEQRES 8 A 120 ILE LEU GLY ALA LYS GLY LYS LEU PHE LYS THR LYS THR SEQRES 9 A 120 GLY GLU LEU SER ILE HIS CYS THR GLU LEU ARG LEU LEU SEQRES 10 A 120 THR LYS ALA HELIX 1 1 GLN A 48 PHE A 53 1 6 HELIX 2 2 ASN A 58 ALA A 63 1 6 HELIX 3 3 GLN A 112 LYS A 115 1 4 SHEET 1 A 3 GLY A 93 VAL A 99 0 SHEET 2 A 3 SER A 84 ASP A 90 -1 N ASP A 90 O GLY A 93 SHEET 3 A 3 ARG A 73 ARG A 77 -1 N THR A 76 O THR A 87 SHEET 1 B 2 LEU A 122 PHE A 129 0 SHEET 2 B 2 SER A 137 LEU A 145 -1 N ARG A 144 O GLY A 123 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