HEADER LIGASE 14-DEC-10 3PZC TITLE CRYSTAL STRUCTURE OF CLASS II AARS HOMOLOGUE (BLL0957) COMPLEXED WITH TITLE 2 COENZYME A COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINO ACID--[ACYL-CARRIER-PROTEIN] LIGASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AMINO ACID:[CARRIER-PROTEIN] LIGASE [AMP FORMING] 1, AA:CP COMPND 5 LIGASE 1, AMINOACYL-[ACYL-CARRIER-PROTEIN] SYNTHETASE 1, L- COMPND 6 GLYCINE:[ACYL-CARRIER-PROTEIN] LIGASE 1; COMPND 7 EC: 6.2.1.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM JAPONICUM; SOURCE 3 ORGANISM_TAXID: 375; SOURCE 4 GENE: BLL0957; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS LIGASE, AMINO ACID:[CARRIER PROTEIN] LIGASE, SERYL-TRNA SYNTHETASE, KEYWDS 2 CARRIER PROTEIN, COENZYME A EXPDTA X-RAY DIFFRACTION AUTHOR I.WEYGAND-DURASEVIC,M.LUIC,M.MOCIBOB,N.IVIC,D.SUBASIC REVDAT 3 20-MAR-24 3PZC 1 REMARK SEQADV LINK REVDAT 2 08-NOV-17 3PZC 1 REMARK REVDAT 1 19-OCT-11 3PZC 0 JRNL AUTH M.MOCIBOB,N.IVIC,D.SUBASIC,M.LUIC,I.WEYGAND-DURASEVIC JRNL TITL SUBSTRATE RECOGNITION BY NOVEL FAMILY OF AMINO ACID:[CARRIER JRNL TITL 2 PROTEIN] LIGASES JRNL REF CROATICA CHEMICA ACTA V. 84 149 2011 JRNL REFN ISSN 0011-1643 JRNL DOI 10.5562/CCA1818 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.MOCIBOB,N.IVIC,S.BILOKAPIC,T.MAIER,M.LUIC,N.BAN, REMARK 1 AUTH 2 I.WEYGAND-DURASEVIC REMARK 1 TITL HOMOLOGS OF AMINOACYL-TRNA SYNTHETASES ACYLATE CARRIER REMARK 1 TITL 2 PROTEINS AND PROVIDE A LINK BETWEEN RIBOSOMAL AND REMARK 1 TITL 3 NONRIBOSOMAL PEPTIDE SYNTHESIS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 107 14585 2010 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 20663952 REMARK 1 DOI 10.1073/PNAS.1007470107 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 32404 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1605 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 20.8636 - 4.8738 0.99 3136 164 0.1587 0.2147 REMARK 3 2 4.8738 - 3.8766 0.99 2969 158 0.1265 0.1683 REMARK 3 3 3.8766 - 3.3889 0.99 2956 152 0.1511 0.1940 REMARK 3 4 3.3889 - 3.0802 0.98 2928 155 0.1558 0.2309 REMARK 3 5 3.0802 - 2.8600 0.96 2840 145 0.1699 0.2078 REMARK 3 6 2.8600 - 2.6917 0.95 2785 148 0.1645 0.2194 REMARK 3 7 2.6917 - 2.5572 0.94 2758 145 0.1719 0.2441 REMARK 3 8 2.5572 - 2.4460 0.91 2679 146 0.1746 0.2465 REMARK 3 9 2.4460 - 2.3520 0.89 2607 135 0.1855 0.2543 REMARK 3 10 2.3520 - 2.2709 0.89 2598 129 0.2039 0.2836 REMARK 3 11 2.2709 - 2.2000 0.87 2543 128 0.2456 0.3138 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 49.83 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.880 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.46630 REMARK 3 B22 (A**2) : 3.91680 REMARK 3 B33 (A**2) : -2.77010 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 4799 REMARK 3 ANGLE : 1.041 6527 REMARK 3 CHIRALITY : 0.068 688 REMARK 3 PLANARITY : 0.005 860 REMARK 3 DIHEDRAL : 18.976 1756 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056 REMARK 200 MONOCHROMATOR : NOVA OPTICAL ASSEMBLY REMARK 200 INCORPORATING GRADED MULTILAYER REMARK 200 OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD RUBY CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : SCALA CCP4_3.3.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32404 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.950 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6755 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) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.17 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17M AMMONIUM ACETATE, 0.085M SODIUM REMARK 280 ACETATE TRIHYDRATE, 25.5% PEG 4000, 15% GLYCEROL, PH 4.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 64.09700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.89550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 64.09700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.89550 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 ILE A 3 REMARK 465 ALA A 4 REMARK 465 VAL A 5 REMARK 465 LEU A 6 REMARK 465 PRO A 7 REMARK 465 ASN A 8 REMARK 465 SER A 9 REMARK 465 PRO A 10 REMARK 465 ASP A 11 REMARK 465 THR A 12 REMARK 465 ALA A 13 REMARK 465 PRO A 14 REMARK 465 GLN A 15 REMARK 465 ILE A 16 REMARK 465 GLN A 313 REMARK 465 PRO A 314 REMARK 465 HIS A 315 REMARK 465 VAL A 316 REMARK 465 ALA A 317 REMARK 465 ALA A 318 REMARK 465 GLY A 319 REMARK 465 ALA A 320 REMARK 465 HIS A 321 REMARK 465 GLY A 322 REMARK 465 GLU A 323 REMARK 465 GLY A 324 REMARK 465 TRP A 325 REMARK 465 ARG A 326 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ILE B 3 REMARK 465 ALA B 4 REMARK 465 VAL B 5 REMARK 465 LEU B 6 REMARK 465 PRO B 7 REMARK 465 ASN B 8 REMARK 465 SER B 9 REMARK 465 PRO B 10 REMARK 465 ASP B 11 REMARK 465 THR B 12 REMARK 465 ALA B 13 REMARK 465 PRO B 14 REMARK 465 GLN B 15 REMARK 465 ILE B 16 REMARK 465 ALA B 17 REMARK 465 SER B 214 REMARK 465 ASP B 215 REMARK 465 PRO B 216 REMARK 465 PHE B 217 REMARK 465 PHE B 218 REMARK 465 GLY B 219 REMARK 465 ARG B 220 REMARK 465 VAL B 221 REMARK 465 GLY B 222 REMARK 465 GLN B 223 REMARK 465 MET B 224 REMARK 465 LYS B 225 REMARK 465 ALA B 226 REMARK 465 VAL B 227 REMARK 465 SER B 228 REMARK 465 GLN B 229 REMARK 465 LYS B 230 REMARK 465 GLN B 231 REMARK 465 GLN B 232 REMARK 465 GLN B 233 REMARK 465 PRO B 314 REMARK 465 HIS B 315 REMARK 465 VAL B 316 REMARK 465 ALA B 317 REMARK 465 ALA B 318 REMARK 465 GLY B 319 REMARK 465 ALA B 320 REMARK 465 HIS B 321 REMARK 465 GLY B 322 REMARK 465 GLU B 323 REMARK 465 GLY B 324 REMARK 465 TRP B 325 REMARK 465 ARG B 326 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 SER A 244 153.78 177.25 REMARK 500 ARG A 258 -132.42 48.40 REMARK 500 ALA B 111 31.61 -99.89 REMARK 500 ASP B 123 32.59 -94.38 REMARK 500 GLU B 161 84.53 -152.78 REMARK 500 TYR B 212 78.79 -116.90 REMARK 500 ARG B 258 -142.12 58.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 COA B 1001 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 A1000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 131 SG REMARK 620 2 GLU A 176 OE1 114.6 REMARK 620 3 CYS A 279 SG 128.5 96.8 REMARK 620 4 GAP A1001 N 109.4 103.8 100.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 131 SG REMARK 620 2 GLU B 176 OE1 108.2 REMARK 620 3 CYS B 279 SG 124.7 97.6 REMARK 620 4 ACT B1002 OXT 115.4 112.1 97.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COA B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MF1 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AN ANALOGUE OF GLYCYL ADENYLATE. REMARK 900 RELATED ID: 3MF2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AMP. REMARK 900 RELATED ID: 3MEY RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ATP. REMARK 900 RELATED ID: 2CJA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE REMARK 900 COMPLEXED WITH ATP. DBREF 3PZC A 1 326 UNP Q89VT8 AACL1_BRAJA 1 326 DBREF 3PZC B 1 326 UNP Q89VT8 AACL1_BRAJA 1 326 SEQADV 3PZC MET A -19 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC GLY A -18 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER A -17 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER A -16 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS A -15 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS A -14 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS A -13 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS A -12 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS A -11 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS A -10 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER A -9 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER A -8 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC GLY A -7 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC LEU A -6 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC VAL A -5 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC PRO A -4 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC ARG A -3 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC GLY A -2 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER A -1 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS A 0 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC MET B -19 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC GLY B -18 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER B -17 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER B -16 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS B -15 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS B -14 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS B -13 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS B -12 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS B -11 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS B -10 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER B -9 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER B -8 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC GLY B -7 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC LEU B -6 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC VAL B -5 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC PRO B -4 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC ARG B -3 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC GLY B -2 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC SER B -1 UNP Q89VT8 EXPRESSION TAG SEQADV 3PZC HIS B 0 UNP Q89VT8 EXPRESSION TAG SEQRES 1 A 346 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 346 LEU VAL PRO ARG GLY SER HIS MET ASN ILE ALA VAL LEU SEQRES 3 A 346 PRO ASN SER PRO ASP THR ALA PRO GLN ILE ALA ASP PRO SEQRES 4 A 346 LEU ASP HIS LEU ALA ASP LYS LEU PHE HIS SER MET GLY SEQRES 5 A 346 SER ASP GLY VAL TYR ALA ARG THR ALA LEU TYR GLU SER SEQRES 6 A 346 ILE VAL GLU ARG LEU ALA ALA LEU ILE THR SER HIS ARG SEQRES 7 A 346 GLU ALA GLY THR GLU ALA LEU ARG PHE PRO PRO VAL MET SEQRES 8 A 346 SER ARG ALA GLN LEU GLU LYS SER GLY TYR LEU LYS SER SEQRES 9 A 346 PHE PRO ASN LEU LEU GLY CYS VAL CYS GLY LEU HIS GLY SEQRES 10 A 346 THR GLU ARG GLU ILE ASN ALA ALA VAL SER ARG PHE ASP SEQRES 11 A 346 ALA GLY GLY ASP TRP THR THR SER LEU SER PRO ALA ASP SEQRES 12 A 346 LEU VAL LEU SER PRO ALA ALA CYS TYR PRO VAL TYR PRO SEQRES 13 A 346 ILE ALA ALA SER ARG GLY PRO LEU PRO LYS GLY GLY LEU SEQRES 14 A 346 ARG PHE ASP VAL ALA ALA ASP CYS PHE ARG ARG GLU PRO SEQRES 15 A 346 SER LYS HIS LEU ASP ARG LEU GLN SER PHE ARG MET ARG SEQRES 16 A 346 GLU TYR VAL CYS ILE GLY THR PRO ASP ASP VAL SER ASP SEQRES 17 A 346 PHE ARG GLU ARG TRP MET VAL ARG ALA GLN ALA ILE ALA SEQRES 18 A 346 ARG ASP LEU GLY LEU THR PHE ARG VAL ASP TYR ALA SER SEQRES 19 A 346 ASP PRO PHE PHE GLY ARG VAL GLY GLN MET LYS ALA VAL SEQRES 20 A 346 SER GLN LYS GLN GLN GLN LEU LYS PHE GLU LEU LEU ILE SEQRES 21 A 346 PRO LEU ARG SER GLU GLU GLN PRO THR ALA CYS MET SER SEQRES 22 A 346 PHE ASN TYR HIS ARG GLU HIS PHE GLY THR THR TRP GLY SEQRES 23 A 346 ILE GLN ASP ALA ASN GLY GLU PRO ALA HIS THR GLY CYS SEQRES 24 A 346 VAL ALA PHE GLY MET ASP ARG LEU ALA VAL ALA MET PHE SEQRES 25 A 346 HIS THR HIS GLY THR ASP LEU SER ALA TRP PRO ALA LYS SEQRES 26 A 346 VAL ARG ASP ILE LEU GLY LEU GLN PRO HIS VAL ALA ALA SEQRES 27 A 346 GLY ALA HIS GLY GLU GLY TRP ARG SEQRES 1 B 346 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 346 LEU VAL PRO ARG GLY SER HIS MET ASN ILE ALA VAL LEU SEQRES 3 B 346 PRO ASN SER PRO ASP THR ALA PRO GLN ILE ALA ASP PRO SEQRES 4 B 346 LEU ASP HIS LEU ALA ASP LYS LEU PHE HIS SER MET GLY SEQRES 5 B 346 SER ASP GLY VAL TYR ALA ARG THR ALA LEU TYR GLU SER SEQRES 6 B 346 ILE VAL GLU ARG LEU ALA ALA LEU ILE THR SER HIS ARG SEQRES 7 B 346 GLU ALA GLY THR GLU ALA LEU ARG PHE PRO PRO VAL MET SEQRES 8 B 346 SER ARG ALA GLN LEU GLU LYS SER GLY TYR LEU LYS SER SEQRES 9 B 346 PHE PRO ASN LEU LEU GLY CYS VAL CYS GLY LEU HIS GLY SEQRES 10 B 346 THR GLU ARG GLU ILE ASN ALA ALA VAL SER ARG PHE ASP SEQRES 11 B 346 ALA GLY GLY ASP TRP THR THR SER LEU SER PRO ALA ASP SEQRES 12 B 346 LEU VAL LEU SER PRO ALA ALA CYS TYR PRO VAL TYR PRO SEQRES 13 B 346 ILE ALA ALA SER ARG GLY PRO LEU PRO LYS GLY GLY LEU SEQRES 14 B 346 ARG PHE ASP VAL ALA ALA ASP CYS PHE ARG ARG GLU PRO SEQRES 15 B 346 SER LYS HIS LEU ASP ARG LEU GLN SER PHE ARG MET ARG SEQRES 16 B 346 GLU TYR VAL CYS ILE GLY THR PRO ASP ASP VAL SER ASP SEQRES 17 B 346 PHE ARG GLU ARG TRP MET VAL ARG ALA GLN ALA ILE ALA SEQRES 18 B 346 ARG ASP LEU GLY LEU THR PHE ARG VAL ASP TYR ALA SER SEQRES 19 B 346 ASP PRO PHE PHE GLY ARG VAL GLY GLN MET LYS ALA VAL SEQRES 20 B 346 SER GLN LYS GLN GLN GLN LEU LYS PHE GLU LEU LEU ILE SEQRES 21 B 346 PRO LEU ARG SER GLU GLU GLN PRO THR ALA CYS MET SER SEQRES 22 B 346 PHE ASN TYR HIS ARG GLU HIS PHE GLY THR THR TRP GLY SEQRES 23 B 346 ILE GLN ASP ALA ASN GLY GLU PRO ALA HIS THR GLY CYS SEQRES 24 B 346 VAL ALA PHE GLY MET ASP ARG LEU ALA VAL ALA MET PHE SEQRES 25 B 346 HIS THR HIS GLY THR ASP LEU SER ALA TRP PRO ALA LYS SEQRES 26 B 346 VAL ARG ASP ILE LEU GLY LEU GLN PRO HIS VAL ALA ALA SEQRES 27 B 346 GLY ALA HIS GLY GLU GLY TRP ARG HET ZN A1000 1 HET GAP A1001 27 HET GOL A1010 6 HET GOL A1011 6 HET ZN B1000 1 HET COA B1001 35 HET ACT B1004 4 HET ACT B1003 4 HET ACT B1002 4 HETNAM ZN ZINC ION HETNAM GAP GLYCYL-ADENOSINE-5'-PHOSPHATE HETNAM GOL GLYCEROL HETNAM COA COENZYME A HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 GAP C12 H17 N6 O8 P FORMUL 5 GOL 2(C3 H8 O3) FORMUL 8 COA C21 H36 N7 O16 P3 S FORMUL 9 ACT 3(C2 H3 O2 1-) FORMUL 12 HOH *322(H2 O) HELIX 1 1 LEU A 20 HIS A 22 5 3 HELIX 2 2 LEU A 23 LEU A 27 1 5 HELIX 3 3 THR A 40 SER A 56 1 17 HELIX 4 4 ARG A 73 SER A 79 1 7 HELIX 5 5 GLY A 80 SER A 84 5 5 HELIX 6 6 PHE A 85 LEU A 89 5 5 HELIX 7 7 THR A 98 ALA A 111 1 14 HELIX 8 8 ASP A 114 LEU A 119 5 6 HELIX 9 9 PRO A 133 SER A 140 1 8 HELIX 10 10 THR A 182 LEU A 204 1 23 HELIX 11 11 PHE A 218 GLN A 232 1 15 HELIX 12 12 GLU A 259 GLY A 266 1 8 HELIX 13 13 MET A 284 GLY A 296 1 13 HELIX 14 14 ASP A 298 TRP A 302 5 5 HELIX 15 15 PRO A 303 LEU A 310 1 8 HELIX 16 16 LEU B 20 HIS B 22 5 3 HELIX 17 17 LEU B 23 LEU B 27 1 5 HELIX 18 18 ALA B 41 HIS B 57 1 17 HELIX 19 19 ARG B 73 SER B 79 1 7 HELIX 20 20 GLY B 80 PHE B 85 1 6 HELIX 21 21 PRO B 86 LEU B 89 5 4 HELIX 22 22 THR B 98 ALA B 111 1 14 HELIX 23 23 ASP B 114 LEU B 119 5 6 HELIX 24 24 PRO B 133 SER B 140 1 8 HELIX 25 25 THR B 182 LEU B 204 1 23 HELIX 26 26 GLU B 259 GLY B 266 1 8 HELIX 27 27 MET B 284 GLY B 296 1 13 HELIX 28 28 ASP B 298 TRP B 302 5 5 HELIX 29 29 PRO B 303 LEU B 310 1 8 SHEET 1 A 2 PHE A 28 SER A 30 0 SHEET 2 A 2 TYR A 37 ARG A 39 -1 O ALA A 38 N HIS A 29 SHEET 1 B 9 ARG A 209 TYR A 212 0 SHEET 2 B 9 LYS A 235 ILE A 240 -1 O LEU A 239 N ARG A 209 SHEET 3 B 9 THR A 249 TYR A 256 -1 O THR A 249 N ILE A 240 SHEET 4 B 9 HIS A 276 GLY A 283 -1 O CYS A 279 N ASN A 255 SHEET 5 B 9 SER A 171 GLY A 181 -1 N GLY A 181 O HIS A 276 SHEET 6 B 9 LEU A 149 PHE A 158 -1 N VAL A 153 O GLU A 176 SHEET 7 B 9 THR A 62 ARG A 66 1 N GLU A 63 O ASP A 152 SHEET 8 B 9 VAL B 36 THR B 40 -1 O ARG B 39 N ARG A 66 SHEET 9 B 9 PHE B 28 SER B 33 -1 N HIS B 29 O ALA B 38 SHEET 1 C 6 VAL A 70 SER A 72 0 SHEET 2 C 6 SER A 120 LEU A 126 -1 O VAL A 125 N MET A 71 SHEET 3 C 6 CYS A 91 GLY A 94 -1 N VAL A 92 O ALA A 122 SHEET 4 C 6 GLY B 90 GLY B 94 -1 O CYS B 91 N CYS A 93 SHEET 5 C 6 SER B 120 LEU B 126 -1 O LEU B 126 N GLY B 90 SHEET 6 C 6 VAL B 70 SER B 72 -1 N MET B 71 O VAL B 125 SHEET 1 D 7 THR B 62 ARG B 66 0 SHEET 2 D 7 LEU B 149 PHE B 158 1 O ASP B 152 N LEU B 65 SHEET 3 D 7 SER B 171 GLY B 181 -1 O PHE B 172 N CYS B 157 SHEET 4 D 7 HIS B 276 GLY B 283 -1 O HIS B 276 N GLY B 181 SHEET 5 D 7 THR B 249 TYR B 256 -1 N ASN B 255 O CYS B 279 SHEET 6 D 7 PHE B 236 ILE B 240 -1 N ILE B 240 O THR B 249 SHEET 7 D 7 ARG B 209 ASP B 211 -1 N ARG B 209 O LEU B 239 LINK SG CYS A 131 ZN ZN A1000 1555 1555 2.40 LINK OE1 GLU A 176 ZN ZN A1000 1555 1555 2.05 LINK SG CYS A 279 ZN ZN A1000 1555 1555 2.41 LINK ZN ZN A1000 N GAP A1001 1555 1555 2.23 LINK SG CYS B 131 ZN ZN B1000 1555 1555 2.34 LINK OE1 GLU B 176 ZN ZN B1000 1555 1555 2.12 LINK SG CYS B 279 ZN ZN B1000 1555 1555 2.43 LINK ZN ZN B1000 OXT ACT B1002 1555 1555 2.11 SITE 1 AC1 4 CYS A 131 GLU A 176 CYS A 279 GAP A1001 SITE 1 AC2 20 ARG A 159 GLU A 161 LEU A 169 PHE A 172 SITE 2 AC2 20 MET A 174 GLU A 176 LYS A 235 ALA A 250 SITE 3 AC2 20 CYS A 251 MET A 252 SER A 253 CYS A 279 SITE 4 AC2 20 GLY A 283 ARG A 286 HOH A 352 HOH A 432 SITE 5 AC2 20 HOH A 444 HOH A 457 ZN A1000 GOL A1011 SITE 1 AC3 4 ARG A 39 GLU A 44 ARG A 173 ASP A 285 SITE 1 AC4 8 ARG A 168 PRO A 216 GLU A 237 ARG A 286 SITE 2 AC4 8 HOH A 352 HOH A 432 HOH A 475 GAP A1001 SITE 1 AC5 4 CYS B 131 GLU B 176 CYS B 279 ACT B1002 SITE 1 AC6 20 ARG B 159 GLU B 161 ASP B 167 ARG B 168 SITE 2 AC6 20 LEU B 169 PHE B 172 MET B 174 LYS B 235 SITE 3 AC6 20 GLU B 237 SER B 253 ASN B 255 ALA B 281 SITE 4 AC6 20 ARG B 286 HOH B 327 HOH B 340 HOH B 461 SITE 5 AC6 20 HOH B 480 HOH B 494 ACT B1002 ACT B1003 SITE 1 AC7 2 SER B 45 HOH B 491 SITE 1 AC8 8 MET B 174 ALA B 250 CYS B 251 MET B 252 SITE 2 AC8 8 SER B 253 ALA B 281 GLY B 283 COA B1001 SITE 1 AC9 7 GLU B 176 ASN B 255 HIS B 257 CYS B 279 SITE 2 AC9 7 HOH B 327 ZN B1000 COA B1001 CRYST1 128.194 101.791 50.623 90.00 90.00 90.00 P 21 21 2 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 0.007801 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019754 0.00000