HEADER LIGASE 09-APR-18 5ZNK TITLE CRYSTAL STRUCTURE OF A BACTERIAL PRORS WITH LIGANDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROLYL-TRNA SYNTHETASE,PRORS; COMPND 5 EC: 6.1.1.15; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: MRSA(R3708); SOURCE 5 GENE: PROS, CT123_02285; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMINOACYL-TRNA SYNTHETASE, PROTEIN BIOSYNTHESIS, INHIBITOR, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR B.CHENG,Y.YU,H.ZHOU REVDAT 3 29-NOV-23 5ZNK 1 REMARK REVDAT 2 25-JAN-23 5ZNK 1 JRNL LINK REVDAT 1 29-MAY-19 5ZNK 0 JRNL AUTH B.CHENG,Z.CAI,Z.LUO,S.LUO,Z.LUO,Y.CHENG,Y.YU,J.GUO,Y.JU, JRNL AUTH 2 Q.GU,J.XU,X.JIANG,G.LI,H.ZHOU JRNL TITL STRUCTURE-GUIDED DESIGN OF HALOFUGINONE DERIVATIVES AS JRNL TITL 2 ATP-AIDED INHIBITORS AGAINST BACTERIAL PROLYL-TRNA JRNL TITL 3 SYNTHETASE. JRNL REF J.MED.CHEM. V. 65 15840 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36394909 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01496 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 40645 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 + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2202 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2994 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4377 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.946 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4541 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4260 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6157 ; 1.259 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9775 ; 0.906 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 563 ; 6.300 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 215 ;37.180 ;24.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 763 ;13.462 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;12.905 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 687 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5246 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1037 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2255 ; 0.972 ; 2.675 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2254 ; 0.972 ; 2.675 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2817 ; 1.708 ; 4.006 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2818 ; 1.708 ; 4.006 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2286 ; 0.878 ; 2.700 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2287 ; 0.878 ; 2.699 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3341 ; 1.557 ; 4.023 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4900 ; 3.188 ;20.183 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4901 ; 3.188 ;20.182 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 43 REMARK 3 ORIGIN FOR THE GROUP (A): -18.2749 -1.5974 20.3420 REMARK 3 T TENSOR REMARK 3 T11: 0.0732 T22: 0.0708 REMARK 3 T33: 0.0354 T12: 0.0383 REMARK 3 T13: -0.0299 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 1.6022 L22: 1.3168 REMARK 3 L33: 0.5417 L12: 1.3450 REMARK 3 L13: -0.3611 L23: -0.0251 REMARK 3 S TENSOR REMARK 3 S11: -0.0136 S12: 0.0148 S13: 0.1217 REMARK 3 S21: -0.0917 S22: -0.0666 S23: 0.1685 REMARK 3 S31: -0.0768 S32: -0.0957 S33: 0.0802 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 44 A 188 REMARK 3 ORIGIN FOR THE GROUP (A): 5.0661 1.5292 32.7512 REMARK 3 T TENSOR REMARK 3 T11: 0.0569 T22: 0.0572 REMARK 3 T33: 0.0335 T12: -0.0170 REMARK 3 T13: 0.0025 T23: 0.0145 REMARK 3 L TENSOR REMARK 3 L11: 0.3910 L22: 0.1673 REMARK 3 L33: 0.2151 L12: -0.0535 REMARK 3 L13: -0.0618 L23: 0.0419 REMARK 3 S TENSOR REMARK 3 S11: 0.0022 S12: -0.0001 S13: -0.0462 REMARK 3 S21: -0.0080 S22: -0.0230 S23: -0.0043 REMARK 3 S31: -0.0675 S32: 0.0511 S33: 0.0208 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 189 A 481 REMARK 3 ORIGIN FOR THE GROUP (A): 11.4413 9.7270 8.3210 REMARK 3 T TENSOR REMARK 3 T11: 0.0551 T22: 0.0728 REMARK 3 T33: 0.0863 T12: -0.0004 REMARK 3 T13: 0.0226 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 0.0691 L22: 0.1760 REMARK 3 L33: 0.1420 L12: -0.0489 REMARK 3 L13: -0.0147 L23: -0.1121 REMARK 3 S TENSOR REMARK 3 S11: -0.0067 S12: -0.0120 S13: 0.0285 REMARK 3 S21: -0.0598 S22: -0.0692 S23: -0.0975 REMARK 3 S31: 0.0597 S32: 0.0300 S33: 0.0759 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 482 A 567 REMARK 3 ORIGIN FOR THE GROUP (A): -22.8015 -24.7202 19.0241 REMARK 3 T TENSOR REMARK 3 T11: 0.0360 T22: 0.0889 REMARK 3 T33: 0.0335 T12: -0.0280 REMARK 3 T13: 0.0051 T23: -0.0289 REMARK 3 L TENSOR REMARK 3 L11: 2.3837 L22: 1.3605 REMARK 3 L33: 0.0363 L12: 0.6205 REMARK 3 L13: -0.1089 L23: 0.1033 REMARK 3 S TENSOR REMARK 3 S11: -0.0729 S12: 0.0784 S13: -0.2491 REMARK 3 S21: -0.0984 S22: 0.0555 S23: -0.0456 REMARK 3 S31: -0.0005 S32: -0.0358 S33: 0.0174 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5ZNK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-APR-18. REMARK 100 THE DEPOSITION ID IS D_1300007328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42784 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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: 2J3L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32-40% (V/V) PENTAERYTHRITOL REMARK 280 PROPOXYLATE (5/4 PO/OH), 0.1-0.2 M KCL, 50 MM HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 64.78750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.60200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.78750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.60200 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: 7650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 -11.99124 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 72.98651 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 GLY A 327 REMARK 465 ALA A 328 REMARK 465 ASN A 329 REMARK 465 PRO A 330 REMARK 465 GLY A 331 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 ARG A 12 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 17 CD OE1 OE2 REMARK 470 LYS A 123 CD CE NZ REMARK 470 LYS A 126 CD CE NZ REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 SER A 199 OG REMARK 470 ILE A 202 CG1 CG2 CD1 REMARK 470 HIS A 206 ND1 CD2 CE1 NE2 REMARK 470 GLU A 226 CD OE1 OE2 REMARK 470 GLU A 241 CG CD OE1 OE2 REMARK 470 GLU A 256 CG CD OE1 OE2 REMARK 470 LYS A 261 CG CD CE NZ REMARK 470 GLU A 315 CD OE1 OE2 REMARK 470 GLN A 319 CG CD OE1 NE2 REMARK 470 ILE A 337 CG1 CG2 CD1 REMARK 470 ASP A 338 CG OD1 OD2 REMARK 470 LYS A 339 CG CD CE NZ REMARK 470 GLU A 340 CG CD OE1 OE2 REMARK 470 LYS A 342 CD CE NZ REMARK 470 ASP A 378 OD1 OD2 REMARK 470 GLU A 379 CG CD OE1 OE2 REMARK 470 LYS A 391 CD CE NZ REMARK 470 GLU A 403 CD OE1 OE2 REMARK 470 LYS A 431 CD CE NZ REMARK 470 GLU A 486 CD OE1 OE2 REMARK 470 LYS A 498 CG CD CE NZ REMARK 470 ARG A 509 CG CD NE CZ NH1 NH2 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 109 171.68 176.94 REMARK 500 ASN A 243 75.22 -152.51 REMARK 500 GLU A 361 111.42 -166.51 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 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 406 OE2 REMARK 620 2 GLN A 409 OE1 91.1 REMARK 620 3 ANP A 601 O1B 106.0 159.2 REMARK 620 4 ANP A 601 O1A 90.2 106.7 85.3 REMARK 620 5 HOH A 776 O 174.6 87.5 76.4 85.2 REMARK 620 6 HOH A 793 O 93.8 87.4 80.1 165.3 91.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP A 601 O2G REMARK 620 2 ANP A 601 O2B 88.5 REMARK 620 3 HOH A 714 O 95.2 175.9 REMARK 620 4 HOH A 721 O 87.8 87.1 91.5 REMARK 620 5 HOH A 760 O 173.0 85.0 91.1 89.1 REMARK 620 6 HOH A 787 O 92.0 87.8 93.6 174.9 90.5 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 ANP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9G3 A 605 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS DID NOT CLONED THIS GENE FROM THE STANDARD STRAIN OF REMARK 999 STAPHYLOCOCCUS AUREUS, BUT FROM A CLINICALLY DRUG-RESISTANT STRAIN REMARK 999 (MRSA R3708). PRORS OF MRSA R3708 SHOWS THR 230, ALA 278. DBREF1 5ZNK A 1 567 UNP A0A227M497_STAAU DBREF2 5ZNK A A0A227M497 1 567 SEQADV 5ZNK THR A 230 UNP A0A227M49 ALA 230 SEE SEQUENCE DETAILS SEQADV 5ZNK ALA A 278 UNP A0A227M49 VAL 278 SEE SEQUENCE DETAILS SEQRES 1 A 567 MET LYS GLN SER LYS VAL PHE ILE PRO THR MET ARG ASP SEQRES 2 A 567 VAL PRO SER GLU ALA GLU ALA GLN SER HIS ARG LEU LEU SEQRES 3 A 567 LEU LYS SER GLY LEU ILE LYS GLN SER THR SER GLY ILE SEQRES 4 A 567 TYR SER TYR LEU PRO LEU ALA THR ARG VAL LEU ASN ASN SEQRES 5 A 567 ILE THR ALA ILE VAL ARG GLN GLU MET GLU ARG ILE ASP SEQRES 6 A 567 SER VAL GLU ILE LEU MET PRO ALA LEU GLN GLN ALA GLU SEQRES 7 A 567 LEU TRP GLU GLU SER GLY ARG TRP GLY ALA TYR GLY PRO SEQRES 8 A 567 GLU LEU MET ARG LEU GLN ASP ARG HIS GLY ARG GLN PHE SEQRES 9 A 567 ALA LEU GLY PRO THR HIS GLU GLU LEU VAL THR SER ILE SEQRES 10 A 567 VAL ARG ASN GLU LEU LYS SER TYR LYS GLN LEU PRO MET SEQRES 11 A 567 THR LEU PHE GLN ILE GLN SER LYS PHE ARG ASP GLU LYS SEQRES 12 A 567 ARG PRO ARG PHE GLY LEU LEU ARG GLY ARG GLU PHE ILE SEQRES 13 A 567 MET LYS ASP ALA TYR SER PHE HIS ALA ASP GLU ALA SER SEQRES 14 A 567 LEU ASP GLN THR TYR GLN ASP MET TYR GLN ALA TYR SER SEQRES 15 A 567 ARG ILE PHE GLU ARG VAL GLY ILE ASN ALA ARG PRO VAL SEQRES 16 A 567 VAL ALA ASP SER GLY ALA ILE GLY GLY SER HIS THR HIS SEQRES 17 A 567 GLU PHE MET ALA LEU SER ALA ILE GLY GLU ASP THR ILE SEQRES 18 A 567 VAL TYR SER LYS GLU SER ASP TYR THR ALA ASN ILE GLU SEQRES 19 A 567 LYS ALA GLU VAL VAL TYR GLU PRO ASN HIS LYS HIS SER SEQRES 20 A 567 THR VAL GLN PRO LEU GLU LYS ILE GLU THR PRO ASN VAL SEQRES 21 A 567 LYS THR ALA GLN GLU LEU ALA ASP PHE LEU GLY ARG PRO SEQRES 22 A 567 VAL ASP GLU ILE ALA LYS THR MET ILE PHE LYS VAL ASP SEQRES 23 A 567 GLY GLU TYR ILE MET VAL LEU VAL ARG GLY HIS HIS GLU SEQRES 24 A 567 ILE ASN ASP ILE LYS LEU LYS SER TYR PHE GLY THR ASP SEQRES 25 A 567 ASN ILE GLU LEU ALA THR GLN ASP GLU ILE VAL ASN LEU SEQRES 26 A 567 VAL GLY ALA ASN PRO GLY SER LEU GLY PRO VAL ILE ASP SEQRES 27 A 567 LYS GLU ILE LYS ILE TYR ALA ASP ASN PHE VAL GLN ASP SEQRES 28 A 567 LEU ASN ASN LEU VAL VAL GLY ALA ASN GLU ASP GLY TYR SEQRES 29 A 567 HIS LEU ILE ASN VAL ASN VAL GLY ARG ASP PHE ASN VAL SEQRES 30 A 567 ASP GLU TYR GLY ASP PHE ARG PHE ILE LEU GLU GLY GLU SEQRES 31 A 567 LYS LEU SER ASP GLY SER GLY VAL ALA HIS PHE ALA GLU SEQRES 32 A 567 GLY ILE GLU VAL GLY GLN VAL PHE LYS LEU GLY THR LYS SEQRES 33 A 567 TYR SER GLU SER MET ASN ALA THR PHE LEU ASP ASN GLN SEQRES 34 A 567 GLY LYS ALA GLN PRO LEU ILE MET GLY CYS TYR GLY ILE SEQRES 35 A 567 GLY ILE SER ARG THR LEU SER ALA ILE VAL GLU GLN ASN SEQRES 36 A 567 HIS ASP ASP ASN GLY ILE VAL TRP PRO LYS SER VAL THR SEQRES 37 A 567 PRO PHE ASP LEU HIS LEU ILE SER ILE ASN PRO LYS LYS SEQRES 38 A 567 ASP ASP GLN ARG GLU LEU ALA ASP ALA LEU TYR ALA GLU SEQRES 39 A 567 PHE ASN THR LYS PHE ASP VAL LEU TYR ASP ASP ARG GLN SEQRES 40 A 567 GLU ARG ALA GLY VAL LYS PHE ASN ASP ALA ASP LEU ILE SEQRES 41 A 567 GLY LEU PRO LEU ARG ILE VAL VAL GLY LYS ARG ALA SER SEQRES 42 A 567 GLU GLY ILE VAL GLU VAL LYS GLU ARG LEU THR GLY ASP SEQRES 43 A 567 SER GLU GLU VAL HIS ILE ASP ASP LEU MET THR VAL ILE SEQRES 44 A 567 THR ASN LYS TYR ASP ASN LEU LYS HET ANP A 601 31 HET MG A 602 1 HET MG A 603 1 HET GOL A 604 6 HET 9G3 A 605 23 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM 9G3 7-CHLORO-6-FLUORO-3-{2-OXO-3-[(2S)-PIPERIDIN-2- HETNAM 2 9G3 YL]PROPYL}QUINAZOLIN-4(3H)-ONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG 2(MG 2+) FORMUL 5 GOL C3 H8 O3 FORMUL 6 9G3 C16 H17 CL F N3 O2 FORMUL 7 HOH *127(H2 O) HELIX 1 AA1 LYS A 2 VAL A 6 5 5 HELIX 2 AA2 ALA A 20 SER A 29 1 10 HELIX 3 AA3 LEU A 43 ILE A 64 1 22 HELIX 4 AA4 ALA A 77 GLY A 84 1 8 HELIX 5 AA5 GLY A 84 TYR A 89 1 6 HELIX 6 AA6 HIS A 110 ARG A 119 1 10 HELIX 7 AA7 SER A 124 LEU A 128 5 5 HELIX 8 AA8 PHE A 147 GLY A 152 5 6 HELIX 9 AA9 ASP A 166 VAL A 188 1 23 HELIX 10 AB1 THR A 262 GLY A 271 1 10 HELIX 11 AB2 PRO A 273 GLU A 276 5 4 HELIX 12 AB3 ASN A 301 GLY A 310 1 10 HELIX 13 AB4 THR A 318 VAL A 326 1 9 HELIX 14 AB5 PHE A 348 LEU A 352 5 5 HELIX 15 AB6 THR A 415 ASN A 422 1 8 HELIX 16 AB7 ILE A 444 ASN A 455 1 12 HELIX 17 AB8 LYS A 481 ASN A 496 1 16 HELIX 18 AB9 ARG A 509 GLY A 521 1 13 HELIX 19 AC1 ARG A 531 GLU A 534 5 4 HELIX 20 AC2 ILE A 552 ASN A 565 1 14 SHEET 1 AA1 2 ILE A 32 THR A 36 0 SHEET 2 AA1 2 ILE A 39 TYR A 42 -1 O ILE A 39 N SER A 35 SHEET 1 AA210 VAL A 67 GLU A 68 0 SHEET 2 AA210 MET A 130 PHE A 139 1 O THR A 131 N VAL A 67 SHEET 3 AA210 GLU A 154 HIS A 164 -1 O PHE A 155 N LYS A 138 SHEET 4 AA210 ILE A 436 GLY A 443 -1 O TYR A 440 N ALA A 160 SHEET 5 AA210 HIS A 400 GLY A 414 -1 N PHE A 411 O CYS A 439 SHEET 6 AA210 ASP A 219 TYR A 223 -1 N ILE A 221 O ALA A 402 SHEET 7 AA210 THR A 230 ASN A 232 -1 O ALA A 231 N VAL A 222 SHEET 8 AA210 ALA A 192 VAL A 196 1 N VAL A 196 O THR A 230 SHEET 9 AA210 THR A 207 LEU A 213 -1 O GLU A 209 N VAL A 195 SHEET 10 AA210 HIS A 400 GLY A 414 -1 O GLY A 408 N PHE A 210 SHEET 1 AA3 3 LEU A 74 GLN A 76 0 SHEET 2 AA3 3 GLN A 103 LEU A 106 -1 O ALA A 105 N GLN A 75 SHEET 3 AA3 3 ARG A 95 GLN A 97 -1 N LEU A 96 O PHE A 104 SHEET 1 AA4 3 GLU A 253 GLU A 256 0 SHEET 2 AA4 3 TYR A 364 VAL A 369 -1 O HIS A 365 N ILE A 255 SHEET 3 AA4 3 LEU A 355 GLY A 358 -1 N LEU A 355 O VAL A 369 SHEET 1 AA5 5 ILE A 314 LEU A 316 0 SHEET 2 AA5 5 ALA A 278 VAL A 285 -1 N LYS A 284 O GLU A 315 SHEET 3 AA5 5 GLU A 288 ARG A 295 -1 O VAL A 294 N LYS A 279 SHEET 4 AA5 5 LYS A 342 ASP A 346 1 O TYR A 344 N MET A 291 SHEET 5 AA5 5 GLU A 379 GLY A 381 1 O GLU A 379 N ALA A 345 SHEET 1 AA6 2 THR A 424 LEU A 426 0 SHEET 2 AA6 2 ALA A 432 PRO A 434 -1 O GLN A 433 N PHE A 425 SHEET 1 AA7 2 HIS A 456 ASP A 457 0 SHEET 2 AA7 2 GLY A 460 ILE A 461 -1 O GLY A 460 N ASP A 457 SHEET 1 AA8 5 VAL A 501 ASP A 504 0 SHEET 2 AA8 5 LEU A 472 SER A 476 1 N LEU A 474 O ASP A 504 SHEET 3 AA8 5 LEU A 524 VAL A 528 1 O VAL A 528 N ILE A 475 SHEET 4 AA8 5 ILE A 536 GLU A 541 -1 O GLU A 538 N VAL A 527 SHEET 5 AA8 5 SER A 547 HIS A 551 -1 O VAL A 550 N VAL A 537 LINK OE2 GLU A 406 MG MG A 603 1555 1555 2.47 LINK OE1 GLN A 409 MG MG A 603 1555 1555 2.10 LINK O2G ANP A 601 MG MG A 602 1555 1555 1.97 LINK O2B ANP A 601 MG MG A 602 1555 1555 2.17 LINK O1B ANP A 601 MG MG A 603 1555 1555 2.12 LINK O1A ANP A 601 MG MG A 603 1555 1555 2.46 LINK MG MG A 602 O HOH A 714 1555 1555 2.00 LINK MG MG A 602 O HOH A 721 1555 1555 2.10 LINK MG MG A 602 O HOH A 760 1555 1555 2.04 LINK MG MG A 602 O HOH A 787 1555 1555 2.07 LINK MG MG A 603 O HOH A 776 1555 1555 2.51 LINK MG MG A 603 O HOH A 793 1555 1555 2.41 CISPEP 1 LEU A 128 PRO A 129 0 4.87 SITE 1 AC1 26 ARG A 140 GLU A 142 LEU A 149 LEU A 150 SITE 2 AC1 26 ARG A 151 GLY A 152 PHE A 155 MET A 157 SITE 3 AC1 26 GLU A 406 VAL A 407 GLY A 408 GLN A 409 SITE 4 AC1 26 GLY A 443 ARG A 446 MG A 602 MG A 603 SITE 5 AC1 26 GOL A 604 9G3 A 605 HOH A 714 HOH A 719 SITE 6 AC1 26 HOH A 721 HOH A 760 HOH A 776 HOH A 783 SITE 7 AC1 26 HOH A 787 HOH A 793 SITE 1 AC2 5 ANP A 601 HOH A 714 HOH A 721 HOH A 760 SITE 2 AC2 5 HOH A 787 SITE 1 AC3 5 GLU A 406 GLN A 409 ANP A 601 HOH A 776 SITE 2 AC3 5 HOH A 793 SITE 1 AC4 7 GLU A 209 ASP A 219 ASN A 232 GLU A 234 SITE 2 AC4 7 GLU A 406 ANP A 601 HOH A 808 SITE 1 AC5 14 TRP A 80 ARG A 85 TYR A 89 GLU A 92 SITE 2 AC5 14 LEU A 93 PRO A 108 THR A 109 GLU A 111 SITE 3 AC5 14 ARG A 140 ASP A 159 TYR A 161 GLY A 441 SITE 4 AC5 14 ANP A 601 HOH A 760 CRYST1 129.575 77.204 73.965 90.00 99.33 90.00 C 1 2 1 4 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 0.007718 0.000000 0.001268 0.00000 SCALE2 0.000000 0.012953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013701 0.00000