HEADER LIGASE 27-JAN-99 1B8A TITLE ASPARTYL-TRNA SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ASPARTYL-TRNA SYNTHETASE); COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ASPARTYL TRNA LIGASE; COMPND 5 EC: 6.1.1.12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: ASPS; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PUC18F KEYWDS SYNTHETASE, TRNA LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SCHMITT,L.MOULINIER,J.-C.THIERRY,D.MORAS REVDAT 8 09-AUG-23 1B8A 1 REMARK LINK REVDAT 7 04-OCT-17 1B8A 1 REMARK REVDAT 6 13-JUL-11 1B8A 1 VERSN REVDAT 5 24-FEB-09 1B8A 1 VERSN REVDAT 4 01-APR-03 1B8A 1 JRNL REVDAT 3 06-MAR-00 1B8A 1 COMPND HEADER CRYST1 DBREF REVDAT 3 2 1 SEQADV REVDAT 2 09-FEB-99 1B8A 1 REMARK REVDAT 1 02-FEB-99 1B8A 0 JRNL AUTH E.SCHMITT,L.MOULINIER,S.FUJIWARA,T.IMANAKA,J.C.THIERRY, JRNL AUTH 2 D.MORAS JRNL TITL CRYSTAL STRUCTURE OF ASPARTYL-TRNA SYNTHETASE FROM JRNL TITL 2 PYROCOCCUS KODAKARAENSIS KOD: ARCHAEON SPECIFICITY AND JRNL TITL 3 CATALYTIC MECHANISM OF ADENYLATE FORMATION. JRNL REF EMBO J. V. 17 5227 1998 JRNL REFN ISSN 0261-4189 JRNL PMID 9724658 JRNL DOI 10.1093/EMBOJ/17.17.5227 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 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) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 101060 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) : 0.168 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5102 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 14554 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 784 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7188 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 1230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.12000 REMARK 3 B22 (A**2) : -2.26000 REMARK 3 B33 (A**2) : -3.87000 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) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.050 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) : 0.880 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.490 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.240 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 50.70 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 : DNAMULTLUC.PARAM REMARK 3 PARAMETER FILE 3 : LIGAND.PARAM REMARK 3 PARAMETER FILE 4 : PARAM19.ION REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_OLD.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3916674 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 5.00000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1ASZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 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 62.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 62.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 62.50000 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: 11420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH B 2582 O HOH B 2917 2.14 REMARK 500 O HOH B 2731 O HOH B 2958 2.14 REMARK 500 O HOH A 2968 O HOH A 2985 2.15 REMARK 500 O HOH A 2828 O HOH A 2956 2.18 REMARK 500 O HOH B 2616 O HOH B 2937 2.18 REMARK 500 O HOH A 2975 O HOH A 3115 2.18 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 ALA A 168 N - CA - C ANGL. DEV. = -19.9 DEGREES REMARK 500 PRO A 347 C - N - CA ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 371 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B1371 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B1371 NE - CZ - NH2 ANGL. DEV. = -3.9 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 THR A 167 -177.65 172.11 REMARK 500 ALA A 168 -47.70 175.41 REMARK 500 THR A 169 45.80 39.63 REMARK 500 GLU A 170 17.45 -68.00 REMARK 500 PHE A 181 -123.16 55.15 REMARK 500 SER A 190 146.92 -170.13 REMARK 500 ASP A 204 -43.46 61.90 REMARK 500 LYS A 346 72.51 -158.38 REMARK 500 ARG A 351 46.96 -84.91 REMARK 500 PHE B1181 -114.95 57.33 REMARK 500 SER B1190 146.50 178.15 REMARK 500 ASP B1204 -45.32 64.66 REMARK 500 LYS B1346 74.64 -162.01 REMARK 500 ARG B1351 45.47 -87.04 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 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 361 OE2 REMARK 620 2 SER A 364 OG 82.1 REMARK 620 3 ATP A 500 O1A 96.0 89.5 REMARK 620 4 ATP A 500 O1B 93.1 173.6 86.7 REMARK 620 5 HOH A2250 O 97.2 88.9 166.5 95.9 REMARK 620 6 HOH A2251 O 164.4 82.3 82.6 102.3 83.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 361 OE1 REMARK 620 2 ATP A 500 O2G 101.7 REMARK 620 3 ATP A 500 O1B 102.8 87.1 REMARK 620 4 HOH A2248 O 77.3 94.2 178.6 REMARK 620 5 HOH A2249 O 163.1 93.6 84.9 94.7 REMARK 620 6 HOH A2250 O 78.8 177.2 90.1 88.6 86.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 600 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 500 O3G REMARK 620 2 ATP A 500 O2B 97.3 REMARK 620 3 HOH A2198 O 89.0 173.7 REMARK 620 4 HOH A2199 O 174.9 85.0 88.9 REMARK 620 5 HOH A2200 O 97.7 87.7 90.6 86.9 REMARK 620 6 HOH A2201 O 90.1 96.9 83.8 85.1 170.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B1361 OE1 REMARK 620 2 ATP B1500 O1B 112.4 REMARK 620 3 ATP B1500 O1G 104.5 87.0 REMARK 620 4 HOH B2252 O 155.5 86.9 90.9 REMARK 620 5 HOH B2254 O 75.6 91.4 178.3 89.5 REMARK 620 6 HOH B2293 O 78.7 168.9 90.0 82.5 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B1361 OE2 REMARK 620 2 SER B1364 OG 99.2 REMARK 620 3 ATP B1500 O1A 100.6 85.1 REMARK 620 4 ATP B1500 O1B 95.9 162.8 84.0 REMARK 620 5 HOH B2253 O 171.2 72.1 79.8 92.9 REMARK 620 6 HOH B2254 O 95.2 89.6 163.9 97.3 84.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1600 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B1500 O2B REMARK 620 2 ATP B1500 O2G 93.9 REMARK 620 3 HOH B2194 O 172.5 92.2 REMARK 620 4 HOH B2195 O 99.0 90.2 85.4 REMARK 620 5 HOH B2196 O 87.5 95.5 87.5 171.1 REMARK 620 6 HOH B2197 O 87.6 176.0 86.6 85.9 88.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 1600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 1602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 1500 DBREF 1B8A A 1 438 UNP Q52428 SYD_PYRKO 1 438 DBREF 1B8A B 1001 1438 UNP Q52428 SYD_PYRKO 1 438 SEQADV 1B8A ASN A 122 UNP Q52428 ASP 122 CONFLICT SEQADV 1B8A GLU A 189 UNP Q52428 GLN 189 CONFLICT SEQADV 1B8A GLU A 196 UNP Q52428 GLN 196 CONFLICT SEQADV 1B8A LEU A 413 UNP Q52428 VAL 413 CONFLICT SEQADV 1B8A ASN B 1122 UNP Q52428 ASP 122 CONFLICT SEQADV 1B8A GLU B 1189 UNP Q52428 GLN 189 CONFLICT SEQADV 1B8A GLU B 1196 UNP Q52428 GLN 196 CONFLICT SEQADV 1B8A LEU B 1413 UNP Q52428 VAL 413 CONFLICT SEQRES 1 A 438 MET TYR ARG THR HIS TYR SER SER GLU ILE THR GLU GLU SEQRES 2 A 438 LEU ASN GLY GLN LYS VAL LYS VAL ALA GLY TRP VAL TRP SEQRES 3 A 438 GLU VAL LYS ASP LEU GLY GLY ILE LYS PHE LEU TRP ILE SEQRES 4 A 438 ARG ASP ARG ASP GLY ILE VAL GLN ILE THR ALA PRO LYS SEQRES 5 A 438 LYS LYS VAL ASP PRO GLU LEU PHE LYS LEU ILE PRO LYS SEQRES 6 A 438 LEU ARG SER GLU ASP VAL VAL ALA VAL GLU GLY VAL VAL SEQRES 7 A 438 ASN PHE THR PRO LYS ALA LYS LEU GLY PHE GLU ILE LEU SEQRES 8 A 438 PRO GLU LYS ILE VAL VAL LEU ASN ARG ALA GLU THR PRO SEQRES 9 A 438 LEU PRO LEU ASP PRO THR GLY LYS VAL LYS ALA GLU LEU SEQRES 10 A 438 ASP THR ARG LEU ASN ASN ARG PHE MET ASP LEU ARG ARG SEQRES 11 A 438 PRO GLU VAL MET ALA ILE PHE LYS ILE ARG SER SER VAL SEQRES 12 A 438 PHE LYS ALA VAL ARG ASP PHE PHE HIS GLU ASN GLY PHE SEQRES 13 A 438 ILE GLU ILE HIS THR PRO LYS ILE ILE ALA THR ALA THR SEQRES 14 A 438 GLU GLY GLY THR GLU LEU PHE PRO MET LYS TYR PHE GLU SEQRES 15 A 438 GLU ASP ALA PHE LEU ALA GLU SER PRO GLN LEU TYR LYS SEQRES 16 A 438 GLU ILE MET MET ALA SER GLY LEU ASP ARG VAL TYR GLU SEQRES 17 A 438 ILE ALA PRO ILE PHE ARG ALA GLU GLU HIS ASN THR THR SEQRES 18 A 438 ARG HIS LEU ASN GLU ALA TRP SER ILE ASP SER GLU MET SEQRES 19 A 438 ALA PHE ILE GLU ASP GLU GLU GLU VAL MET SER PHE LEU SEQRES 20 A 438 GLU ARG LEU VAL ALA HIS ALA ILE ASN TYR VAL ARG GLU SEQRES 21 A 438 HIS ASN ALA LYS GLU LEU ASP ILE LEU ASN PHE GLU LEU SEQRES 22 A 438 GLU GLU PRO LYS LEU PRO PHE PRO ARG VAL SER TYR ASP SEQRES 23 A 438 LYS ALA LEU GLU ILE LEU GLY ASP LEU GLY LYS GLU ILE SEQRES 24 A 438 PRO TRP GLY GLU ASP ILE ASP THR GLU GLY GLU ARG LEU SEQRES 25 A 438 LEU GLY LYS TYR MET MET GLU ASN GLU ASN ALA PRO LEU SEQRES 26 A 438 TYR PHE LEU TYR GLN TYR PRO SER GLU ALA LYS PRO PHE SEQRES 27 A 438 TYR ILE MET LYS TYR ASP ASN LYS PRO GLU ILE CYS ARG SEQRES 28 A 438 ALA PHE ASP LEU GLU TYR ARG GLY VAL GLU ILE SER SER SEQRES 29 A 438 GLY GLY GLN ARG GLU HIS ARG HIS ASP ILE LEU VAL GLU SEQRES 30 A 438 GLN ILE LYS GLU LYS GLY LEU ASN PRO GLU SER PHE GLU SEQRES 31 A 438 PHE TYR LEU LYS ALA PHE ARG TYR GLY MET PRO PRO HIS SEQRES 32 A 438 GLY GLY PHE GLY LEU GLY ALA GLU ARG LEU ILE LYS GLN SEQRES 33 A 438 MET LEU ASP LEU PRO ASN ILE ARG GLU VAL ILE LEU PHE SEQRES 34 A 438 PRO ARG ASP ARG ARG ARG LEU THR PRO SEQRES 1 B 438 MET TYR ARG THR HIS TYR SER SER GLU ILE THR GLU GLU SEQRES 2 B 438 LEU ASN GLY GLN LYS VAL LYS VAL ALA GLY TRP VAL TRP SEQRES 3 B 438 GLU VAL LYS ASP LEU GLY GLY ILE LYS PHE LEU TRP ILE SEQRES 4 B 438 ARG ASP ARG ASP GLY ILE VAL GLN ILE THR ALA PRO LYS SEQRES 5 B 438 LYS LYS VAL ASP PRO GLU LEU PHE LYS LEU ILE PRO LYS SEQRES 6 B 438 LEU ARG SER GLU ASP VAL VAL ALA VAL GLU GLY VAL VAL SEQRES 7 B 438 ASN PHE THR PRO LYS ALA LYS LEU GLY PHE GLU ILE LEU SEQRES 8 B 438 PRO GLU LYS ILE VAL VAL LEU ASN ARG ALA GLU THR PRO SEQRES 9 B 438 LEU PRO LEU ASP PRO THR GLY LYS VAL LYS ALA GLU LEU SEQRES 10 B 438 ASP THR ARG LEU ASN ASN ARG PHE MET ASP LEU ARG ARG SEQRES 11 B 438 PRO GLU VAL MET ALA ILE PHE LYS ILE ARG SER SER VAL SEQRES 12 B 438 PHE LYS ALA VAL ARG ASP PHE PHE HIS GLU ASN GLY PHE SEQRES 13 B 438 ILE GLU ILE HIS THR PRO LYS ILE ILE ALA THR ALA THR SEQRES 14 B 438 GLU GLY GLY THR GLU LEU PHE PRO MET LYS TYR PHE GLU SEQRES 15 B 438 GLU ASP ALA PHE LEU ALA GLU SER PRO GLN LEU TYR LYS SEQRES 16 B 438 GLU ILE MET MET ALA SER GLY LEU ASP ARG VAL TYR GLU SEQRES 17 B 438 ILE ALA PRO ILE PHE ARG ALA GLU GLU HIS ASN THR THR SEQRES 18 B 438 ARG HIS LEU ASN GLU ALA TRP SER ILE ASP SER GLU MET SEQRES 19 B 438 ALA PHE ILE GLU ASP GLU GLU GLU VAL MET SER PHE LEU SEQRES 20 B 438 GLU ARG LEU VAL ALA HIS ALA ILE ASN TYR VAL ARG GLU SEQRES 21 B 438 HIS ASN ALA LYS GLU LEU ASP ILE LEU ASN PHE GLU LEU SEQRES 22 B 438 GLU GLU PRO LYS LEU PRO PHE PRO ARG VAL SER TYR ASP SEQRES 23 B 438 LYS ALA LEU GLU ILE LEU GLY ASP LEU GLY LYS GLU ILE SEQRES 24 B 438 PRO TRP GLY GLU ASP ILE ASP THR GLU GLY GLU ARG LEU SEQRES 25 B 438 LEU GLY LYS TYR MET MET GLU ASN GLU ASN ALA PRO LEU SEQRES 26 B 438 TYR PHE LEU TYR GLN TYR PRO SER GLU ALA LYS PRO PHE SEQRES 27 B 438 TYR ILE MET LYS TYR ASP ASN LYS PRO GLU ILE CYS ARG SEQRES 28 B 438 ALA PHE ASP LEU GLU TYR ARG GLY VAL GLU ILE SER SER SEQRES 29 B 438 GLY GLY GLN ARG GLU HIS ARG HIS ASP ILE LEU VAL GLU SEQRES 30 B 438 GLN ILE LYS GLU LYS GLY LEU ASN PRO GLU SER PHE GLU SEQRES 31 B 438 PHE TYR LEU LYS ALA PHE ARG TYR GLY MET PRO PRO HIS SEQRES 32 B 438 GLY GLY PHE GLY LEU GLY ALA GLU ARG LEU ILE LYS GLN SEQRES 33 B 438 MET LEU ASP LEU PRO ASN ILE ARG GLU VAL ILE LEU PHE SEQRES 34 B 438 PRO ARG ASP ARG ARG ARG LEU THR PRO HET MN A 600 1 HET MN A 601 1 HET MN A 602 1 HET ATP A 500 31 HET MN B1600 1 HET MN B1601 1 HET MN B1602 1 HET ATP B1500 31 HETNAM MN MANGANESE (II) ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 3 MN 6(MN 2+) FORMUL 6 ATP 2(C10 H16 N5 O13 P3) FORMUL 11 HOH *1230(H2 O) HELIX 1 1 SER A 7 GLU A 9 5 3 HELIX 2 2 GLU A 12 LEU A 14 5 3 HELIX 3 3 PRO A 57 LYS A 65 1 9 HELIX 4 4 LEU A 117 ARG A 129 1 13 HELIX 5 5 PRO A 131 ASN A 154 1 24 HELIX 6 6 GLN A 192 ALA A 200 1 9 HELIX 7 7 GLU A 240 HIS A 261 1 22 HELIX 8 8 ALA A 263 ILE A 268 1 6 HELIX 9 9 TYR A 285 ASP A 294 1 10 HELIX 10 10 THR A 307 GLU A 321 1 15 HELIX 11 11 SER A 333 ALA A 335 5 3 HELIX 12 12 HIS A 372 GLU A 381 1 10 HELIX 13 13 PRO A 386 PHE A 396 5 11 HELIX 14 14 ALA A 410 MET A 417 1 8 HELIX 15 15 ILE A 423 VAL A 426 5 4 HELIX 16 16 SER B 1007 GLU B 1009 5 3 HELIX 17 17 GLU B 1012 LEU B 1014 5 3 HELIX 18 18 LYS B 1052 LYS B 1054 5 3 HELIX 19 19 PRO B 1057 LYS B 1065 1 9 HELIX 20 20 LEU B 1117 ARG B 1129 1 13 HELIX 21 21 PRO B 1131 ASN B 1154 1 24 HELIX 22 22 GLN B 1192 ALA B 1200 1 9 HELIX 23 23 GLU B 1240 HIS B 1261 1 22 HELIX 24 24 ALA B 1263 ILE B 1268 1 6 HELIX 25 25 TYR B 1285 LEU B 1295 1 11 HELIX 26 26 THR B 1307 GLU B 1321 1 15 HELIX 27 27 SER B 1333 ALA B 1335 5 3 HELIX 28 28 HIS B 1372 GLU B 1381 1 10 HELIX 29 29 PRO B 1386 PHE B 1396 5 11 HELIX 30 30 ALA B 1410 MET B 1417 1 8 HELIX 31 31 ILE B 1423 GLU B 1425 5 3 SHEET 1 A 5 PHE A 88 PRO A 92 0 SHEET 2 A 5 VAL A 71 PHE A 80 -1 N ASN A 79 O GLU A 89 SHEET 3 A 5 LYS A 18 LEU A 31 -1 N GLY A 23 O VAL A 72 SHEET 4 A 5 ILE A 34 ASP A 41 -1 N ARG A 40 O TRP A 24 SHEET 5 A 5 GLY A 44 PRO A 51 -1 N ALA A 50 O LYS A 35 SHEET 1 B 2 PRO A 177 TYR A 180 0 SHEET 2 B 2 GLU A 183 PHE A 186 -1 N ALA A 185 O MET A 178 SHEET 1 C 7 ARG A 205 PHE A 213 0 SHEET 2 C 7 GLU A 226 ALA A 235 -1 N GLU A 233 O VAL A 206 SHEET 3 C 7 HIS A 403 GLY A 409 -1 N LEU A 408 O ILE A 230 SHEET 4 C 7 VAL A 360 GLN A 367 -1 N GLY A 366 O GLY A 405 SHEET 5 C 7 ALA A 352 TYR A 357 -1 N TYR A 357 O VAL A 360 SHEET 6 C 7 LEU A 325 TYR A 329 -1 N LEU A 328 O ASP A 354 SHEET 7 C 7 PRO A 281 SER A 284 1 N PRO A 281 O PHE A 327 SHEET 1 D 2 VAL A 71 GLU A 75 0 SHEET 2 D 2 LYS A 94 ASN A 99 -1 N ASN A 99 O VAL A 71 SHEET 1 E 5 PHE B1088 PRO B1092 0 SHEET 2 E 5 VAL B1071 PHE B1080 -1 N ASN B1079 O GLU B1089 SHEET 3 E 5 LYS B1018 ASP B1030 -1 N GLY B1023 O VAL B1072 SHEET 4 E 5 ILE B1034 ASP B1041 -1 N ARG B1040 O TRP B1024 SHEET 5 E 5 GLY B1044 PRO B1051 -1 N ALA B1050 O LYS B1035 SHEET 1 F 2 PRO B1177 TYR B1180 0 SHEET 2 F 2 GLU B1183 PHE B1186 -1 N ALA B1185 O MET B1178 SHEET 1 G 7 ARG B1205 PHE B1213 0 SHEET 2 G 7 GLU B1226 ALA B1235 -1 N GLU B1233 O VAL B1206 SHEET 3 G 7 HIS B1403 GLY B1409 -1 N LEU B1408 O ILE B1230 SHEET 4 G 7 VAL B1360 GLN B1367 -1 N GLY B1366 O GLY B1405 SHEET 5 G 7 ALA B1352 TYR B1357 -1 N TYR B1357 O VAL B1360 SHEET 6 G 7 LEU B1325 TYR B1329 -1 N LEU B1328 O ASP B1354 SHEET 7 G 7 PRO B1281 SER B1284 1 N PRO B1281 O PHE B1327 SHEET 1 H 2 VAL B1071 GLU B1075 0 SHEET 2 H 2 LYS B1094 ASN B1099 -1 N ASN B1099 O VAL B1071 LINK OE2 GLU A 361 MN MN A 601 1555 1555 2.42 LINK OE1 GLU A 361 MN MN A 602 1555 1555 2.20 LINK OG SER A 364 MN MN A 601 1555 1555 2.37 LINK O3G ATP A 500 MN MN A 600 1555 1555 2.21 LINK O2B ATP A 500 MN MN A 600 1555 1555 2.18 LINK O1A ATP A 500 MN MN A 601 1555 1555 2.59 LINK O1B ATP A 500 MN MN A 601 1555 1555 2.17 LINK O2G ATP A 500 MN MN A 602 1555 1555 2.25 LINK O1B ATP A 500 MN MN A 602 1555 1555 2.33 LINK MN MN A 600 O HOH A2198 1555 1555 2.30 LINK MN MN A 600 O HOH A2199 1555 1555 2.26 LINK MN MN A 600 O HOH A2200 1555 1555 2.36 LINK MN MN A 600 O HOH A2201 1555 1555 2.29 LINK MN MN A 601 O HOH A2250 1555 1555 2.41 LINK MN MN A 601 O HOH A2251 1555 1555 2.62 LINK MN MN A 602 O HOH A2248 1555 1555 2.48 LINK MN MN A 602 O HOH A2249 1555 1555 2.38 LINK MN MN A 602 O HOH A2250 1555 1555 2.48 LINK OE1 GLU B1361 MN MN B1601 1555 1555 2.21 LINK OE2 GLU B1361 MN MN B1602 1555 1555 2.46 LINK OG SER B1364 MN MN B1602 1555 1555 2.63 LINK O2B ATP B1500 MN MN B1600 1555 1555 2.26 LINK O2G ATP B1500 MN MN B1600 1555 1555 2.18 LINK O1B ATP B1500 MN MN B1601 1555 1555 2.34 LINK O1G ATP B1500 MN MN B1601 1555 1555 2.19 LINK O1A ATP B1500 MN MN B1602 1555 1555 2.57 LINK O1B ATP B1500 MN MN B1602 1555 1555 2.29 LINK MN MN B1600 O HOH B2194 1555 1555 2.24 LINK MN MN B1600 O HOH B2195 1555 1555 2.42 LINK MN MN B1600 O HOH B2196 1555 1555 2.26 LINK MN MN B1600 O HOH B2197 1555 1555 2.19 LINK MN MN B1601 O HOH B2252 1555 1555 2.46 LINK MN MN B1601 O HOH B2254 1555 1555 2.47 LINK MN MN B1601 O HOH B2293 1555 1555 2.73 LINK MN MN B1602 O HOH B2253 1555 1555 2.62 LINK MN MN B1602 O HOH B2254 1555 1555 2.30 CISPEP 1 THR A 103 PRO A 104 0 -0.14 CISPEP 2 LEU A 278 PRO A 279 0 -0.23 CISPEP 3 THR A 437 PRO A 438 0 0.19 CISPEP 4 THR B 1103 PRO B 1104 0 0.07 CISPEP 5 LEU B 1278 PRO B 1279 0 -0.49 CISPEP 6 THR B 1437 PRO B 1438 0 -0.53 SITE 1 AC1 5 ATP A 500 HOH A2198 HOH A2199 HOH A2200 SITE 2 AC1 5 HOH A2201 SITE 1 AC2 6 GLU A 361 SER A 364 ATP A 500 MN A 602 SITE 2 AC2 6 HOH A2250 HOH A2251 SITE 1 AC3 6 GLU A 361 ATP A 500 MN A 601 HOH A2248 SITE 2 AC3 6 HOH A2249 HOH A2250 SITE 1 AC4 5 ATP B1500 HOH B2194 HOH B2195 HOH B2196 SITE 2 AC4 5 HOH B2197 SITE 1 AC5 6 GLU B1361 ATP B1500 MN B1602 HOH B2252 SITE 2 AC5 6 HOH B2254 HOH B2293 SITE 1 AC6 6 GLU B1361 SER B1364 ATP B1500 MN B1601 SITE 2 AC6 6 HOH B2253 HOH B2254 SITE 1 AC7 20 ARG A 214 GLU A 216 ARG A 222 HIS A 223 SITE 2 AC7 20 LEU A 224 GLU A 361 ILE A 362 SER A 363 SITE 3 AC7 20 SER A 364 GLY A 407 GLY A 409 ARG A 412 SITE 4 AC7 20 MN A 600 MN A 601 MN A 602 HOH A2148 SITE 5 AC7 20 HOH A2191 HOH A2199 HOH A2200 HOH A3114 SITE 1 AC8 19 ARG B1214 GLU B1216 HIS B1223 LEU B1224 SITE 2 AC8 19 ALA B1227 GLU B1361 ILE B1362 SER B1363 SITE 3 AC8 19 SER B1364 GLY B1407 GLY B1409 ARG B1412 SITE 4 AC8 19 MN B1600 MN B1601 MN B1602 HOH B2123 SITE 5 AC8 19 HOH B2196 HOH B2197 HOH B2987 CRYST1 124.800 125.000 87.160 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 0.008013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011473 0.00000 MTRIX1 1 -0.065100 0.996700 -0.049000 4.47940 1 MTRIX2 1 0.996600 0.062400 -0.053800 -4.05430 1 MTRIX3 1 -0.050500 -0.052300 -0.997400 5.97950 1