HEADER LIGASE 28-APR-15 4ZIB TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF PYLRS MUTANT BOUND WITH TITLE 2 3-BENZOTHIENYL-L-ALANINE AND ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 185-454); COMPND 5 SYNONYM: PYRROLYSINE--TRNA(PYL) LIGASE,PYRROLYSYL-TRNA SYNTHETASE, COMPND 6 PYLRS; COMPND 7 EC: 6.1.1.26; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI (STRAIN ATCC BAA-159 / DSM SOURCE 3 3647 / GOE1 / GO1 / JCM 11833 / OCM 88); SOURCE 4 ORGANISM_TAXID: 192952; SOURCE 5 STRAIN: ATCC BAA-159 / DSM 3647 / GOE1 / GO1 / JCM 11833 / OCM 88; SOURCE 6 GENE: PYLS, MM_1445; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 CODON PLUS RIL (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS AMINOACYL-TRNA SYNTHETASES, ARCHAEAL PROTEINS, EVOLUTION, MOLECULAR, KEYWDS 2 GENETIC CODE, SUBSTRATE SPECIFICITY, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.NAKAMURA,L.T.GUO,Y.S.WANG,D.SOLL REVDAT 4 15-NOV-23 4ZIB 1 ATOM REVDAT 3 27-SEP-23 4ZIB 1 REMARK REVDAT 2 14-OCT-20 4ZIB 1 REMARK LINK ATOM REVDAT 1 02-MAR-16 4ZIB 0 JRNL AUTH M.ENGLERT,A.NAKAMURA,Y.S.WANG,D.EILER,D.SOLL,L.T.GUO JRNL TITL PROBING THE ACTIVE SITE TRYPTOPHAN OF STAPHYLOCOCCUS AUREUS JRNL TITL 2 THIOREDOXIN WITH AN ANALOG. JRNL REF NUCLEIC ACIDS RES. V. 43 11061 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26582921 JRNL DOI 10.1093/NAR/GKV1255 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 27795 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2803 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 42.2415 - 5.5704 1.00 1299 148 0.1497 0.1467 REMARK 3 2 5.5704 - 4.4229 1.00 1263 153 0.1310 0.1636 REMARK 3 3 4.4229 - 3.8643 1.00 1262 153 0.1320 0.1543 REMARK 3 4 3.8643 - 3.5111 1.00 1264 130 0.1530 0.1727 REMARK 3 5 3.5111 - 3.2596 1.00 1238 155 0.1729 0.2044 REMARK 3 6 3.2596 - 3.0675 1.00 1268 147 0.1706 0.2043 REMARK 3 7 3.0675 - 2.9139 1.00 1266 139 0.1860 0.2423 REMARK 3 8 2.9139 - 2.7871 1.00 1231 153 0.1920 0.2209 REMARK 3 9 2.7871 - 2.6798 1.00 1256 135 0.2023 0.2561 REMARK 3 10 2.6798 - 2.5873 1.00 1255 141 0.2013 0.2447 REMARK 3 11 2.5873 - 2.5064 1.00 1244 143 0.1964 0.2582 REMARK 3 12 2.5064 - 2.4348 1.00 1265 135 0.2057 0.2437 REMARK 3 13 2.4348 - 2.3707 1.00 1269 128 0.2081 0.2291 REMARK 3 14 2.3707 - 2.3129 1.00 1246 138 0.2163 0.2564 REMARK 3 15 2.3129 - 2.2603 0.96 1211 119 0.2356 0.2649 REMARK 3 16 2.2603 - 2.2122 0.94 1189 131 0.3175 0.3687 REMARK 3 17 2.2122 - 2.1679 1.00 1261 133 0.2256 0.2635 REMARK 3 18 2.1679 - 2.1270 1.00 1241 128 0.2017 0.2284 REMARK 3 19 2.1270 - 2.0891 1.00 1265 149 0.2006 0.2429 REMARK 3 20 2.0891 - 2.0536 0.98 1199 145 0.2330 0.2780 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.003 2244 REMARK 3 ANGLE : 0.772 3019 REMARK 3 CHIRALITY : 0.028 321 REMARK 3 PLANARITY : 0.003 400 REMARK 3 DIHEDRAL : 14.096 893 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 4ZIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27798 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 42.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 19.71 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 20.20 REMARK 200 R MERGE FOR SHELL (I) : 0.63400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.750 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2ZIM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, MGCL2, PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.64000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.28000 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.64000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.28000 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: 5000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 52.57000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 91.05391 REMARK 350 BIOMT3 2 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 164 REMARK 465 GLY A 165 REMARK 465 SER A 166 REMARK 465 SER A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 SER A 174 REMARK 465 SER A 175 REMARK 465 GLY A 176 REMARK 465 LEU A 177 REMARK 465 VAL A 178 REMARK 465 PRO A 179 REMARK 465 ARG A 180 REMARK 465 GLY A 181 REMARK 465 SER A 182 REMARK 465 HIS A 183 REMARK 465 MET A 184 REMARK 465 ALA A 185 REMARK 465 SER A 186 REMARK 465 ALA A 187 REMARK 465 ILE A 208 REMARK 465 SER A 209 REMARK 465 LEU A 210 REMARK 465 ASN A 211 REMARK 465 ASP A 379 REMARK 465 SER A 380 REMARK 465 CYS A 381 REMARK 465 MET A 382 REMARK 465 VAL A 383 REMARK 465 TYR A 384 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 A 675 O HOH A 703 2.19 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 GLU A 237 -92.85 -109.13 REMARK 500 ASP A 292 -146.71 55.61 REMARK 500 ALA A 315 -34.73 -133.69 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 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 396 OE2 REMARK 620 2 SER A 399 OG 80.6 REMARK 620 3 ATP A 504 O1A 92.4 91.5 REMARK 620 4 ATP A 504 O1B 88.2 167.8 93.7 REMARK 620 5 HOH A 686 O 102.4 90.1 165.1 87.7 REMARK 620 6 HOH A 702 O 176.0 96.1 85.3 95.3 79.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 396 OE1 REMARK 620 2 ATP A 504 O3G 94.7 REMARK 620 3 ATP A 504 O1B 87.4 80.5 REMARK 620 4 HOH A 659 O 155.0 94.6 71.4 REMARK 620 5 HOH A 686 O 78.1 152.7 72.9 83.1 REMARK 620 6 HOH A 726 O 95.9 117.4 161.3 100.3 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 504 O2G REMARK 620 2 ATP A 504 O2B 94.1 REMARK 620 3 HOH A 607 O 94.7 93.9 REMARK 620 4 HOH A 660 O 88.1 176.2 82.8 REMARK 620 5 HOH A 662 O 176.2 84.0 88.7 94.0 REMARK 620 6 HOH A 693 O 87.1 95.7 170.1 87.5 89.8 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 MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4OG A 512 DBREF 4ZIB A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 4ZIB MET A 164 UNP Q8PWY1 INITIATING METHIONINE SEQADV 4ZIB GLY A 165 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB SER A 166 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB SER A 167 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB HIS A 168 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB HIS A 169 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB HIS A 170 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB HIS A 171 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB HIS A 172 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB HIS A 173 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB SER A 174 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB SER A 175 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB GLY A 176 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB LEU A 177 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB VAL A 178 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB PRO A 179 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB ARG A 180 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB MET A 184 UNP Q8PWY1 EXPRESSION TAG SEQADV 4ZIB GLY A 346 UNP Q8PWY1 ASN 346 ENGINEERED MUTATION SEQADV 4ZIB GLN A 348 UNP Q8PWY1 CYS 348 ENGINEERED MUTATION SEQRES 1 A 291 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 291 LEU VAL PRO ARG GLY SER HIS MET ALA SER ALA PRO ALA SEQRES 3 A 291 LEU THR LYS SER GLN THR ASP ARG LEU GLU VAL LEU LEU SEQRES 4 A 291 ASN PRO LYS ASP GLU ILE SER LEU ASN SER GLY LYS PRO SEQRES 5 A 291 PHE ARG GLU LEU GLU SER GLU LEU LEU SER ARG ARG LYS SEQRES 6 A 291 LYS ASP LEU GLN GLN ILE TYR ALA GLU GLU ARG GLU ASN SEQRES 7 A 291 TYR LEU GLY LYS LEU GLU ARG GLU ILE THR ARG PHE PHE SEQRES 8 A 291 VAL ASP ARG GLY PHE LEU GLU ILE LYS SER PRO ILE LEU SEQRES 9 A 291 ILE PRO LEU GLU TYR ILE GLU ARG MET GLY ILE ASP ASN SEQRES 10 A 291 ASP THR GLU LEU SER LYS GLN ILE PHE ARG VAL ASP LYS SEQRES 11 A 291 ASN PHE CYS LEU ARG PRO MET LEU ALA PRO ASN LEU TYR SEQRES 12 A 291 ASN TYR LEU ARG LYS LEU ASP ARG ALA LEU PRO ASP PRO SEQRES 13 A 291 ILE LYS ILE PHE GLU ILE GLY PRO CYS TYR ARG LYS GLU SEQRES 14 A 291 SER ASP GLY LYS GLU HIS LEU GLU GLU PHE THR MET LEU SEQRES 15 A 291 GLY PHE GLN GLN MET GLY SER GLY CYS THR ARG GLU ASN SEQRES 16 A 291 LEU GLU SER ILE ILE THR ASP PHE LEU ASN HIS LEU GLY SEQRES 17 A 291 ILE ASP PHE LYS ILE VAL GLY ASP SER CYS MET VAL TYR SEQRES 18 A 291 GLY ASP THR LEU ASP VAL MET HIS GLY ASP LEU GLU LEU SEQRES 19 A 291 SER SER ALA VAL VAL GLY PRO ILE PRO LEU ASP ARG GLU SEQRES 20 A 291 TRP GLY ILE ASP LYS PRO TRP ILE GLY ALA GLY PHE GLY SEQRES 21 A 291 LEU GLU ARG LEU LEU LYS VAL LYS HIS ASP PHE LYS ASN SEQRES 22 A 291 ILE LYS ARG ALA ALA ARG SER GLU SER TYR TYR ASN GLY SEQRES 23 A 291 ILE SER THR ASN LEU HET MG A 501 1 HET MG A 502 1 HET MG A 503 1 HET ATP A 504 31 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 509 4 HET EDO A 510 4 HET EDO A 511 4 HET 4OG A 512 15 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM 4OG 3-(1-BENZOTHIOPHEN-3-YL)-L-ALANINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG 3(MG 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 EDO 7(C2 H6 O2) FORMUL 13 4OG C11 H11 N O2 S FORMUL 14 HOH *139(H2 O) HELIX 1 AA1 THR A 191 LEU A 202 1 12 HELIX 2 AA2 PRO A 215 GLU A 237 1 23 HELIX 3 AA3 ASN A 241 ARG A 257 1 17 HELIX 4 AA4 LEU A 270 MET A 276 1 7 HELIX 5 AA5 GLU A 283 GLN A 287 5 5 HELIX 6 AA6 LEU A 301 ASP A 313 1 13 HELIX 7 AA7 THR A 355 GLY A 371 1 17 HELIX 8 AA8 ILE A 405 GLY A 412 5 8 HELIX 9 AA9 LEU A 424 HIS A 432 1 9 HELIX 10 AB1 ASN A 436 ALA A 441 5 6 SHEET 1 AA1 7 LEU A 260 ILE A 262 0 SHEET 2 AA1 7 ILE A 320 TYR A 329 1 O PHE A 323 N ILE A 262 SHEET 3 AA1 7 GLU A 341 MET A 350 -1 O PHE A 342 N CYS A 328 SHEET 4 AA1 7 TRP A 417 GLY A 423 -1 O PHE A 422 N LEU A 345 SHEET 5 AA1 7 LEU A 395 VAL A 402 -1 N VAL A 401 O GLY A 419 SHEET 6 AA1 7 ASP A 386 HIS A 392 -1 N LEU A 388 O ALA A 400 SHEET 7 AA1 7 LYS A 375 VAL A 377 -1 N VAL A 377 O ASP A 389 SHEET 1 AA2 3 LEU A 267 PRO A 269 0 SHEET 2 AA2 3 PHE A 295 LEU A 297 -1 O CYS A 296 N ILE A 268 SHEET 3 AA2 3 ARG A 290 VAL A 291 -1 N VAL A 291 O PHE A 295 SHEET 1 AA3 2 TYR A 446 TYR A 447 0 SHEET 2 AA3 2 ILE A 450 SER A 451 -1 O ILE A 450 N TYR A 447 LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.41 LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.52 LINK OG SER A 399 MG MG A 502 1555 1555 2.21 LINK MG MG A 501 O2G ATP A 504 1555 1555 2.13 LINK MG MG A 501 O2B ATP A 504 1555 1555 2.11 LINK MG MG A 501 O HOH A 607 1555 1555 2.13 LINK MG MG A 501 O HOH A 660 1555 1555 2.04 LINK MG MG A 501 O HOH A 662 1555 1555 2.08 LINK MG MG A 501 O HOH A 693 1555 1555 2.25 LINK MG MG A 502 O1A ATP A 504 1555 1555 2.31 LINK MG MG A 502 O1B ATP A 504 1555 1555 2.15 LINK MG MG A 502 O HOH A 686 1555 1555 2.12 LINK MG MG A 502 O HOH A 702 1555 1555 2.21 LINK MG MG A 503 O3G ATP A 504 1555 1555 2.14 LINK MG MG A 503 O1B ATP A 504 1555 1555 2.42 LINK MG MG A 503 O HOH A 659 1555 1555 2.36 LINK MG MG A 503 O HOH A 686 1555 1555 2.56 LINK MG MG A 503 O HOH A 726 1555 1555 2.47 CISPEP 1 ASP A 318 PRO A 319 0 -1.10 CISPEP 2 GLY A 403 PRO A 404 0 1.94 SITE 1 AC1 5 ATP A 504 HOH A 607 HOH A 660 HOH A 662 SITE 2 AC1 5 HOH A 693 SITE 1 AC2 6 GLU A 396 SER A 399 MG A 503 ATP A 504 SITE 2 AC2 6 HOH A 686 HOH A 702 SITE 1 AC3 6 GLU A 396 MG A 502 ATP A 504 HOH A 659 SITE 2 AC3 6 HOH A 686 HOH A 726 SITE 1 AC4 26 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC4 26 PHE A 342 MET A 344 GLU A 396 LEU A 397 SITE 3 AC4 26 SER A 398 SER A 399 GLY A 421 GLY A 423 SITE 4 AC4 26 ARG A 426 MG A 501 MG A 502 MG A 503 SITE 5 AC4 26 EDO A 510 HOH A 607 HOH A 651 HOH A 659 SITE 6 AC4 26 HOH A 660 HOH A 662 HOH A 674 HOH A 686 SITE 7 AC4 26 HOH A 693 HOH A 702 SITE 1 AC5 6 ASN A 241 ARG A 439 ALA A 440 ASN A 448 SITE 2 AC5 6 GLY A 449 HOH A 612 SITE 1 AC6 4 TYR A 242 GLU A 249 LYS A 431 HIS A 432 SITE 1 AC7 3 ASP A 256 ARG A 257 HIS A 369 SITE 1 AC8 5 ASP A 373 LYS A 375 HIS A 392 GLY A 393 SITE 2 AC8 5 HOH A 663 SITE 1 AC9 7 ASP A 313 MET A 350 GLY A 412 ILE A 413 SITE 2 AC9 7 ASP A 414 LYS A 415 HOH A 605 SITE 1 AD1 5 HIS A 338 ASP A 394 GLU A 396 ARG A 426 SITE 2 AD1 5 ATP A 504 SITE 1 AD2 6 TYR A 272 ASN A 307 ARG A 310 LYS A 311 SITE 2 AD2 6 GLU A 357 GLU A 444 SITE 1 AD3 7 MET A 300 LEU A 301 ALA A 302 LEU A 305 SITE 2 AD3 7 MET A 344 SER A 399 HOH A 651 CRYST1 105.140 105.140 70.920 90.00 90.00 120.00 P 64 6 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 0.009511 0.005491 0.000000 0.00000 SCALE2 0.000000 0.010983 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014100 0.00000