HEADER SYNTHETASE 31-JAN-03 1OBH TITLE LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A PRE- TITLE 2 TRANSFER EDITING SUBSTRATE ANALOGUE IN BOTH SYNTHETIC ACTIVE SITE AND TITLE 3 EDITING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ENZYME CONTAINS 878 RESIDUES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 STRAIN: HB27; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SYNTHETASE, AMINOACYL-TRNA SYNTHETASE, CLASS I AMINOACYL-TRNA KEYWDS 2 SYNTHETASE, ATP + L-LEUCINE + TRNA (LEU) -> AMP + PPI L- LEUCYL- KEYWDS 3 TRNA(LEU) EXPDTA X-RAY DIFFRACTION AUTHOR S.CUSACK,A.YAREMCHUK,M.TUKALO REVDAT 4 20-NOV-24 1OBH 1 REMARK REVDAT 3 13-DEC-23 1OBH 1 LINK REVDAT 2 24-FEB-09 1OBH 1 VERSN REVDAT 1 09-MAY-03 1OBH 0 JRNL AUTH T.LINCECUM,M.TUKALO,A.YAREMCHUK,R.MURSINNA,A.WILLIAMS, JRNL AUTH 2 B.SPROAT,W.VAN DEN EYNDE,A.LINK,S.VAN CALENBERGH,M.GROTLI, JRNL AUTH 3 S.MARTINIS,S.CUSACK JRNL TITL STRUCTURAL AND MECHANISTIC BASIS OF PRE- AND POSTTRANSFER JRNL TITL 2 EDITING BY LEUCYL-TRNA SYNTHETASE JRNL REF MOL.CELL V. 11 951 2003 JRNL REFN ISSN 1097-2765 JRNL PMID 12718881 JRNL DOI 10.1016/S1097-2765(03)00098-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.CUSACK,A.YAREMCHUK,M.TUKALO REMARK 1 TITL THE 2A STRUCTURE OF LEUCYL-TRNA SYNTHETASE AND ITS COMPLEX REMARK 1 TITL 2 WITH A LEUCYL-ADENYLATE ANALOGUE REMARK 1 REF EMBO J. V. 19 2351 2000 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 10811626 REMARK 1 DOI 10.1093/EMBOJ/19.10.2351 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.YAREMCHUK,S.CUSACK,O.GUDZERA,M.GROTLI,M.TUKALO REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF REMARK 1 TITL 2 THERMUS THERMOPHILUS LEUCYL-TRNA SYNTHETASE AND ITS REMARK 1 TITL 3 COMPLEXES WITH LEUCINE AND A NON-HYDROLYSABLE REMARK 1 TITL 4 LEUCYL-ADENYLATE ANALOGUE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 667 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10771445 REMARK 1 DOI 10.1107/S0907444900004686 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 68248 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3388 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9693 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 531 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.21000 REMARK 3 B22 (A**2) : 8.70000 REMARK 3 B33 (A**2) : -1.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.980 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.500 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.750 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.360 ; 4.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 42.17 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA-MULTI-ENDO.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-MULTI-ENDO.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIDE-CHAINS ATOMS WITH NO ELECTRON REMARK 3 DENSITY HAVE ZERO OCCUPANCY.THE ZN1 DOMAIN, RESIDUES 154-189, REMARK 3 ARE DISORDERED IN THIS CRYSTAL FORM. PARTS OF THE ZN2 DOMAIN, REMARK 3 RESIDUES 440-443, 466-470, 486-492 ARE DISORDERED IN THIS REMARK 3 CRYSTAL FORM. THE C-TERMINAL DOMAIN, RESIDUES 815-878, ARE REMARK 3 DISORDERED IN THE CRYSTAL. REMARK 4 REMARK 4 1OBH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1290012074. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68288 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1H3N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN 10 MG/ML IN 50MM BIS-TRIS REMARK 280 PROPANE BUFFER PH 6.0-6.5 2MM DTT, 20MM MGCL2, 1MM NAN3, 18% REMARK 280 AMMONIUM SULPHATE EQUILBRIATED AGAINST 30-38% AMMONIUM SULPHATE REMARK 280 IN 100MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5. SEE REFERENCE 2, PH REMARK 280 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 86.30250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 86.30250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.75750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 76.44200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.75750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 76.44200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 86.30250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.75750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 76.44200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 86.30250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.75750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 76.44200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 32 REMARK 465 GLY A 154 REMARK 465 LEU A 155 REMARK 465 VAL A 156 REMARK 465 ASN A 157 REMARK 465 TRP A 158 REMARK 465 CYS A 159 REMARK 465 PRO A 160 REMARK 465 LYS A 161 REMARK 465 CYS A 162 REMARK 465 GLN A 163 REMARK 465 THR A 164 REMARK 465 VAL A 165 REMARK 465 LEU A 166 REMARK 465 ALA A 167 REMARK 465 ASN A 168 REMARK 465 GLU A 169 REMARK 465 GLN A 170 REMARK 465 VAL A 171 REMARK 465 VAL A 172 REMARK 465 GLU A 173 REMARK 465 GLY A 174 REMARK 465 ARG A 175 REMARK 465 CYS A 176 REMARK 465 TRP A 177 REMARK 465 ARG A 178 REMARK 465 HIS A 179 REMARK 465 GLU A 180 REMARK 465 ASP A 181 REMARK 465 THR A 182 REMARK 465 PRO A 183 REMARK 465 VAL A 184 REMARK 465 GLU A 185 REMARK 465 LYS A 186 REMARK 465 ARG A 187 REMARK 465 GLU A 188 REMARK 465 LEU A 189 REMARK 465 GLU A 440 REMARK 465 ALA A 441 REMARK 465 CYS A 442 REMARK 465 GLY A 443 REMARK 465 ARG A 466 REMARK 465 PRO A 467 REMARK 465 LYS A 468 REMARK 465 GLY A 469 REMARK 465 LYS A 470 REMARK 465 LYS A 486 REMARK 465 CYS A 487 REMARK 465 GLY A 488 REMARK 465 GLY A 489 REMARK 465 PRO A 490 REMARK 465 ALA A 491 REMARK 465 ASP A 815 REMARK 465 VAL A 816 REMARK 465 VAL A 817 REMARK 465 GLU A 818 REMARK 465 VAL A 819 REMARK 465 ALA A 820 REMARK 465 VAL A 821 REMARK 465 GLN A 822 REMARK 465 VAL A 823 REMARK 465 ASN A 824 REMARK 465 GLY A 825 REMARK 465 ARG A 826 REMARK 465 VAL A 827 REMARK 465 ARG A 828 REMARK 465 GLY A 829 REMARK 465 THR A 830 REMARK 465 ILE A 831 REMARK 465 HIS A 832 REMARK 465 ILE A 833 REMARK 465 PRO A 834 REMARK 465 LYS A 835 REMARK 465 ASP A 836 REMARK 465 ALA A 837 REMARK 465 PRO A 838 REMARK 465 LEU A 839 REMARK 465 GLU A 840 REMARK 465 VAL A 841 REMARK 465 ALA A 842 REMARK 465 ARG A 843 REMARK 465 ALA A 844 REMARK 465 GLU A 845 REMARK 465 ALA A 846 REMARK 465 LEU A 847 REMARK 465 LYS A 848 REMARK 465 VAL A 849 REMARK 465 ARG A 850 REMARK 465 ASN A 851 REMARK 465 VAL A 852 REMARK 465 ARG A 853 REMARK 465 ALA A 854 REMARK 465 HIS A 855 REMARK 465 LEU A 856 REMARK 465 GLU A 857 REMARK 465 GLY A 858 REMARK 465 LYS A 859 REMARK 465 GLU A 860 REMARK 465 VAL A 861 REMARK 465 VAL A 862 REMARK 465 LYS A 863 REMARK 465 GLU A 864 REMARK 465 ILE A 865 REMARK 465 TYR A 866 REMARK 465 VAL A 867 REMARK 465 PRO A 868 REMARK 465 GLY A 869 REMARK 465 LYS A 870 REMARK 465 ILE A 871 REMARK 465 LEU A 872 REMARK 465 ASN A 873 REMARK 465 LEU A 874 REMARK 465 VAL A 875 REMARK 465 VAL A 876 REMARK 465 ARG A 877 REMARK 465 GLY A 878 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 332 CG CD1 CD2 CE1 CE2 CZ OH 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 GLU A 2 -179.56 -67.05 REMARK 500 ALA A 8 -52.93 81.07 REMARK 500 ARG A 195 66.50 -68.47 REMARK 500 ARG A 249 53.64 -119.25 REMARK 500 LEU A 459 177.70 -34.83 REMARK 500 LYS A 460 -20.54 -148.96 REMARK 500 PHE A 479 -65.99 -101.55 REMARK 500 ASP A 513 62.34 -164.45 REMARK 500 GLU A 540 -33.69 -38.57 REMARK 500 PHE A 572 79.05 -103.73 REMARK 500 GLN A 655 -90.65 -117.30 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 HG A1815 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 102 OH REMARK 620 2 CYS A 128 SG 102.0 REMARK 620 3 CYS A 128 O 130.7 83.2 REMARK 620 N 1 2 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A1815 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NVA A1816 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LMS A1817 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NVA A1818 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LMS A1819 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H3N RELATED DB: PDB REMARK 900 LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A REMARK 900 SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE REMARK 900 RELATED ID: 1JZQ RELATED DB: PDB REMARK 900 ISOLEUCYL-TRNA SYNTHETASE COMPLEXED WITH ISOLEUCYL-ADENYLATE REMARK 900 ANALOGUE REMARK 900 RELATED ID: 1JZS RELATED DB: PDB REMARK 900 ISOLEUCYL-TRNA SYNTHETASE COMPLEXED WITH MUPIROCIN REMARK 900 RELATED ID: 1OBC RELATED DB: PDB REMARK 900 LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A REMARK 900 POST-TRANSFER EDITING SUBSTRATE ANALOGUE DBREF 1OBH A 1 878 PDB 1OBH 1OBH 1 878 SEQRES 1 A 878 MET GLU LYS TYR ASN PRO HIS ALA ILE GLU ALA LYS TRP SEQRES 2 A 878 GLN ARG PHE TRP GLU GLU LYS GLY PHE MET LYS ALA LYS SEQRES 3 A 878 ASP LEU PRO GLY GLY ARG GLY LYS GLN TYR VAL LEU VAL SEQRES 4 A 878 MET PHE PRO TYR PRO SER GLY ASP LEU HIS MET GLY HIS SEQRES 5 A 878 LEU LYS ASN TYR THR MET GLY ASP VAL LEU ALA ARG PHE SEQRES 6 A 878 ARG ARG MET GLN GLY TYR GLU VAL LEU HIS PRO MET GLY SEQRES 7 A 878 TRP ASP ALA PHE GLY LEU PRO ALA GLU ASN ALA ALA LEU SEQRES 8 A 878 LYS PHE GLY VAL HIS PRO LYS ASP TRP THR TYR ALA ASN SEQRES 9 A 878 ILE ARG GLN ALA LYS GLU SER LEU ARG LEU MET GLY ILE SEQRES 10 A 878 LEU TYR ASP TRP ASP ARG GLU VAL THR THR CYS GLU PRO SEQRES 11 A 878 GLU TYR TYR ARG TRP ASN GLN TRP ILE PHE LEU LYS MET SEQRES 12 A 878 TRP GLU LYS GLY LEU ALA TYR ARG ALA LYS GLY LEU VAL SEQRES 13 A 878 ASN TRP CYS PRO LYS CYS GLN THR VAL LEU ALA ASN GLU SEQRES 14 A 878 GLN VAL VAL GLU GLY ARG CYS TRP ARG HIS GLU ASP THR SEQRES 15 A 878 PRO VAL GLU LYS ARG GLU LEU GLU GLN TRP TYR LEU ARG SEQRES 16 A 878 ILE THR ALA TYR ALA GLU ARG LEU LEU LYS ASP LEU GLU SEQRES 17 A 878 GLY LEU ASN TRP PRO GLU LYS VAL LYS ALA MET GLN ARG SEQRES 18 A 878 ALA TRP ILE GLY ARG SER GLU GLY ALA GLU ILE LEU PHE SEQRES 19 A 878 PRO VAL GLU GLY LYS GLU VAL ARG ILE PRO VAL PHE THR SEQRES 20 A 878 THR ARG PRO ASP THR LEU PHE GLY ALA THR PHE LEU VAL SEQRES 21 A 878 LEU ALA PRO GLU HIS PRO LEU THR LEU GLU LEU ALA ALA SEQRES 22 A 878 PRO GLU LYS ARG GLU GLU VAL LEU ALA TYR VAL GLU ALA SEQRES 23 A 878 ALA LYS ARG LYS THR GLU ILE GLU ARG GLN ALA GLU GLY SEQRES 24 A 878 ARG GLU LYS THR GLY VAL PHE LEU GLY ALA TYR ALA LEU SEQRES 25 A 878 ASN PRO ALA THR GLY GLU ARG ILE PRO ILE TRP THR ALA SEQRES 26 A 878 ASP TYR VAL LEU PHE GLY TYR GLY THR GLY ALA ILE MET SEQRES 27 A 878 ALA VAL PRO ALA HIS ASP GLN ARG ASP TYR GLU PHE ALA SEQRES 28 A 878 ARG LYS PHE GLY LEU PRO ILE LYS LYS VAL ILE GLU ARG SEQRES 29 A 878 PRO GLY GLU PRO LEU PRO GLU PRO LEU GLU ARG ALA TYR SEQRES 30 A 878 GLU GLU PRO GLY ILE MET VAL ASN SER GLY PRO PHE ASP SEQRES 31 A 878 GLY THR GLU SER GLU GLU GLY LYS ARG LYS VAL ILE ALA SEQRES 32 A 878 TRP LEU GLU GLU LYS GLY LEU GLY LYS GLY ARG VAL THR SEQRES 33 A 878 TYR ARG LEU ARG ASP TRP LEU ILE SER ARG GLN ARG TYR SEQRES 34 A 878 TRP GLY THR PRO ILE PRO MET VAL HIS CYS GLU ALA CYS SEQRES 35 A 878 GLY VAL VAL PRO VAL PRO GLU GLU GLU LEU PRO VAL LEU SEQRES 36 A 878 LEU PRO ASP LEU LYS ASP VAL GLU ASP ILE ARG PRO LYS SEQRES 37 A 878 GLY LYS SER PRO LEU GLU ALA HIS PRO GLU PHE TYR GLU SEQRES 38 A 878 THR THR CYS PRO LYS CYS GLY GLY PRO ALA LYS ARG ASP SEQRES 39 A 878 THR ASP THR MET ASP THR PHE PHE ASP SER SER TRP TYR SEQRES 40 A 878 TYR LEU ARG TYR THR ASP PRO HIS ASN ASP ARG LEU PRO SEQRES 41 A 878 PHE ASP PRO GLU LYS ALA ASN ALA TRP MET PRO VAL ASP SEQRES 42 A 878 GLN TYR ILE GLY GLY VAL GLU HIS ALA VAL LEU HIS LEU SEQRES 43 A 878 LEU TYR SER ARG PHE PHE THR LYS PHE LEU HIS ASP LEU SEQRES 44 A 878 GLY MET VAL LYS VAL GLU GLU PRO PHE GLN GLY LEU PHE SEQRES 45 A 878 THR GLN GLY MET VAL LEU ALA TRP THR ASP PHE GLY PRO SEQRES 46 A 878 VAL GLU VAL GLU GLY SER VAL VAL ARG LEU PRO GLU PRO SEQRES 47 A 878 THR ARG ILE ARG LEU GLU ILE PRO GLU SER ALA LEU SER SEQRES 48 A 878 LEU GLU ASP VAL ARG LYS MET GLY ALA GLU LEU ARG PRO SEQRES 49 A 878 HIS GLU ASP GLY THR LEU HIS LEU TRP LYS PRO ALA VAL SEQRES 50 A 878 MET SER LYS SER LYS GLY ASN GLY VAL MET VAL GLY PRO SEQRES 51 A 878 PHE VAL LYS GLU GLN GLY ALA ASP ILE ALA ARG ILE THR SEQRES 52 A 878 ILE LEU PHE ALA ALA PRO PRO GLU ASN GLU MET VAL TRP SEQRES 53 A 878 THR GLU GLU GLY VAL GLN GLY ALA TRP ARG PHE LEU ASN SEQRES 54 A 878 ARG ILE TYR ARG ARG VAL ALA GLU ASP ARG GLU ALA LEU SEQRES 55 A 878 LEU GLU THR SER GLY VAL PHE GLN ALA GLU ALA LEU GLU SEQRES 56 A 878 GLY LYS ASP ARG GLU LEU TYR GLY LYS LEU HIS GLU THR SEQRES 57 A 878 LEU LYS LYS VAL THR GLU ASP LEU GLU ALA LEU ARG PHE SEQRES 58 A 878 ASN THR ALA ILE ALA ALA LEU MET GLU PHE LEU ASN ALA SEQRES 59 A 878 LEU TYR GLU TYR ARG LYS ASP ARG PRO VAL THR PRO VAL SEQRES 60 A 878 TYR ARG THR ALA ILE ARG TYR TYR LEU GLN MET LEU PHE SEQRES 61 A 878 PRO PHE ALA PRO HIS LEU ALA GLU GLU LEU TRP HIS TRP SEQRES 62 A 878 PHE TRP PRO ASP SER LEU PHE GLU ALA GLY TRP PRO GLU SEQRES 63 A 878 LEU ASP GLU LYS ALA LEU GLU LYS ASP VAL VAL GLU VAL SEQRES 64 A 878 ALA VAL GLN VAL ASN GLY ARG VAL ARG GLY THR ILE HIS SEQRES 65 A 878 ILE PRO LYS ASP ALA PRO LEU GLU VAL ALA ARG ALA GLU SEQRES 66 A 878 ALA LEU LYS VAL ARG ASN VAL ARG ALA HIS LEU GLU GLY SEQRES 67 A 878 LYS GLU VAL VAL LYS GLU ILE TYR VAL PRO GLY LYS ILE SEQRES 68 A 878 LEU ASN LEU VAL VAL ARG GLY HET SO4 A1501 5 HET SO4 A1502 5 HET SO4 A1503 5 HET SO4 A1504 5 HET SO4 A1505 5 HET SO4 A1506 5 HET HG A1815 1 HET NVA A1816 7 HET LMS A1817 23 HET NVA A1818 7 HET LMS A1819 23 HETNAM SO4 SULFATE ION HETNAM HG MERCURY (II) ION HETNAM NVA NORVALINE HETNAM LMS [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 2 LMS DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE FORMUL 2 SO4 6(O4 S 2-) FORMUL 8 HG HG 2+ FORMUL 9 NVA 2(C5 H11 N O2) FORMUL 10 LMS 2(C10 H14 N6 O6 S) FORMUL 13 HOH *197(H2 O) HELIX 1 1 ALA A 8 GLY A 21 1 14 HELIX 2 2 HIS A 49 GLY A 70 1 22 HELIX 3 3 GLY A 83 GLY A 94 1 12 HELIX 4 4 HIS A 96 MET A 115 1 20 HELIX 5 5 ASP A 120 GLU A 124 5 5 HELIX 6 6 GLU A 129 LYS A 146 1 18 HELIX 7 7 ILE A 196 ALA A 198 5 3 HELIX 8 8 TYR A 199 ASP A 206 1 8 HELIX 9 9 PRO A 213 GLY A 225 1 13 HELIX 10 10 ARG A 249 ALA A 256 5 8 HELIX 11 11 ALA A 273 GLU A 275 5 3 HELIX 12 12 LYS A 276 ARG A 289 1 14 HELIX 13 13 THR A 291 GLN A 296 1 6 HELIX 14 14 VAL A 340 HIS A 343 5 4 HELIX 15 15 ASP A 344 GLY A 355 1 12 HELIX 16 16 SER A 386 ASP A 390 5 5 HELIX 17 17 GLU A 393 LYS A 408 1 16 HELIX 18 18 PRO A 448 LEU A 452 5 5 HELIX 19 19 SER A 471 ALA A 475 5 5 HELIX 20 20 HIS A 476 GLU A 481 1 6 HELIX 21 21 ASP A 499 SER A 505 1 7 HELIX 22 22 TRP A 506 TYR A 511 1 6 HELIX 23 23 ASP A 522 MET A 530 1 9 HELIX 24 24 ALA A 542 LEU A 559 1 18 HELIX 25 25 PRO A 596 GLU A 604 1 9 HELIX 26 26 LEU A 612 MET A 618 1 7 HELIX 27 27 MET A 647 GLN A 655 1 9 HELIX 28 28 GLY A 656 ALA A 668 1 13 HELIX 29 29 THR A 677 ASP A 698 1 22 HELIX 30 30 ASP A 698 GLU A 704 1 7 HELIX 31 31 GLN A 710 LEU A 714 5 5 HELIX 32 32 GLU A 715 ALA A 738 1 24 HELIX 33 33 ARG A 740 ARG A 762 1 23 HELIX 34 34 THR A 765 PHE A 780 1 16 HELIX 35 35 ALA A 783 HIS A 792 1 10 HELIX 36 36 SER A 798 GLY A 803 1 6 HELIX 37 37 GLU A 809 GLU A 813 5 5 SHEET 1 AA 4 GLU A 72 LEU A 74 0 SHEET 2 AA 4 LYS A 34 VAL A 39 1 O GLN A 35 N LEU A 74 SHEET 3 AA 4 GLN A 534 GLY A 537 1 O GLN A 534 N LEU A 38 SHEET 4 AA 4 LEU A 571 THR A 573 1 O PHE A 572 N GLY A 537 SHEET 1 AB 3 ALA A 149 ALA A 152 0 SHEET 2 AB 3 GLN A 191 LEU A 194 -1 O GLN A 191 N ALA A 152 SHEET 3 AB 3 TRP A 422 LEU A 423 -1 O TRP A 422 N LEU A 194 SHEET 1 AC 3 ARG A 242 THR A 247 0 SHEET 2 AC 3 ARG A 226 PRO A 235 -1 O ALA A 230 N THR A 247 SHEET 3 AC 3 GLY A 411 TYR A 417 -1 O LYS A 412 N GLU A 231 SHEET 1 AD 4 GLY A 304 LEU A 312 0 SHEET 2 AD 4 ARG A 319 ALA A 325 -1 O ILE A 320 N ALA A 311 SHEET 3 AD 4 PHE A 258 LEU A 261 1 O LEU A 259 N TRP A 323 SHEET 4 AD 4 ALA A 336 ALA A 339 -1 O ILE A 337 N VAL A 260 SHEET 1 AE 2 ILE A 362 GLU A 363 0 SHEET 2 AE 2 ILE A 382 MET A 383 -1 O ILE A 382 N GLU A 363 SHEET 1 AF 3 SER A 425 ARG A 426 0 SHEET 2 AF 3 THR A 497 MET A 498 -1 O THR A 497 N ARG A 426 SHEET 3 AF 3 THR A 432 PRO A 433 -1 O THR A 432 N MET A 498 SHEET 1 AG 2 MET A 436 VAL A 437 0 SHEET 2 AG 2 VAL A 445 PRO A 446 -1 O VAL A 445 N VAL A 437 SHEET 1 AH 4 ALA A 609 SER A 611 0 SHEET 2 AH 4 VAL A 592 ARG A 594 -1 O VAL A 593 N LEU A 610 SHEET 3 AH 4 VAL A 577 GLU A 589 -1 O GLU A 587 N ARG A 594 SHEET 4 AH 4 MET A 674 TRP A 676 1 O MET A 674 N LEU A 578 SHEET 1 AI 5 ALA A 609 SER A 611 0 SHEET 2 AI 5 VAL A 592 ARG A 594 -1 O VAL A 593 N LEU A 610 SHEET 3 AI 5 VAL A 577 GLU A 589 -1 O GLU A 587 N ARG A 594 SHEET 4 AI 5 LEU A 630 VAL A 637 -1 O LEU A 630 N VAL A 586 SHEET 5 AI 5 GLU A 621 PRO A 624 -1 O GLU A 621 N TRP A 633 SSBOND 1 CYS A 439 CYS A 484 1555 1555 2.03 LINK C NVA A1816 N LMS A1817 1555 1555 1.33 LINK C NVA A1818 N LMS A1819 1555 1555 1.33 LINK OH TYR A 102 HG HG A1815 1555 1555 3.39 LINK SG CYS A 128 HG HG A1815 1555 1555 2.55 LINK O CYS A 128 HG HG A1815 1555 1555 3.02 CISPEP 1 GLU A 371 PRO A 372 0 -0.16 CISPEP 2 LEU A 452 PRO A 453 0 0.27 CISPEP 3 MET A 530 PRO A 531 0 -0.31 SITE 1 AC1 5 LEU A 714 GLU A 715 GLY A 716 ARG A 719 SITE 2 AC1 5 LYS A 760 SITE 1 AC2 4 GLY A 707 ARG A 769 ARG A 773 TRP A 795 SITE 1 AC3 5 VAL A 564 GLU A 565 GLU A 566 HOH A2193 SITE 2 AC3 5 HOH A2194 SITE 1 AC4 2 ARG A 759 HOH A2178 SITE 1 AC5 3 ARG A 426 ARG A 428 ASP A 499 SITE 1 AC6 5 HIS A 49 HIS A 52 SER A 639 LYS A 640 SITE 2 AC6 5 HOH A2134 SITE 1 AC7 3 TYR A 102 CYS A 128 GLU A 129 SITE 1 AC8 6 PHE A 41 TYR A 43 ASP A 80 TYR A 535 SITE 2 AC8 6 HIS A 545 LMS A1817 SITE 1 AC9 11 PRO A 42 TYR A 43 GLY A 51 HIS A 52 SITE 2 AC9 11 ASN A 55 TYR A 56 MET A 576 VAL A 577 SITE 3 AC9 11 MET A 638 NVA A1816 HOH A2196 SITE 1 BC1 7 THR A 247 THR A 252 MET A 338 VAL A 340 SITE 2 BC1 7 ASP A 347 LMS A1819 HOH A2077 SITE 1 BC2 11 THR A 247 THR A 248 ARG A 249 TYR A 327 SITE 2 BC2 11 VAL A 328 LEU A 329 TYR A 332 ILE A 337 SITE 3 BC2 11 ASP A 344 NVA A1818 HOH A2197 CRYST1 103.515 152.884 172.605 90.00 90.00 90.00 C 2 2 21 8 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 0.009660 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005793 0.00000