HEADER LIGASE 09-APR-18 5ZNJ 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 5ZNJ 1 REMARK REVDAT 2 25-JAN-23 5ZNJ 1 JRNL LINK REVDAT 1 29-MAY-19 5ZNJ 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. 1.84 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 59229 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3053 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) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4437 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 238 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4384 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 273 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.05000 REMARK 3 B22 (A**2) : 1.62000 REMARK 3 B33 (A**2) : -0.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.72000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.129 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.455 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4625 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4311 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6288 ; 1.175 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9915 ; 0.854 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 5.886 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 219 ;34.598 ;24.612 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 776 ;12.077 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;13.429 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 700 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5318 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1058 ; 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): 2297 ; 0.795 ; 3.270 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2296 ; 0.795 ; 3.270 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2882 ; 1.390 ; 4.898 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2883 ; 1.390 ; 4.898 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2328 ; 0.740 ; 3.299 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2328 ; 0.740 ; 3.299 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3403 ; 1.297 ; 4.929 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5225 ; 4.407 ;25.734 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5225 ; 4.407 ;25.734 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 : 8 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): -18.2258 -2.2630 20.4504 REMARK 3 T TENSOR REMARK 3 T11: 0.0913 T22: 0.1448 REMARK 3 T33: 0.0611 T12: 0.0054 REMARK 3 T13: -0.0590 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 0.6675 L22: 0.6806 REMARK 3 L33: 0.8620 L12: 0.4310 REMARK 3 L13: -0.1782 L23: -0.1896 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: 0.1282 S13: 0.0610 REMARK 3 S21: -0.0709 S22: -0.0396 S23: 0.1083 REMARK 3 S31: -0.0484 S32: -0.1418 S33: 0.0346 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): 5.0386 0.9666 32.8917 REMARK 3 T TENSOR REMARK 3 T11: 0.0917 T22: 0.0896 REMARK 3 T33: 0.0974 T12: -0.0281 REMARK 3 T13: -0.0193 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.2811 L22: 0.1028 REMARK 3 L33: 0.5512 L12: -0.0322 REMARK 3 L13: -0.2646 L23: -0.0276 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: -0.0117 S13: -0.0424 REMARK 3 S21: -0.0341 S22: -0.0107 S23: -0.0180 REMARK 3 S31: -0.0980 S32: 0.1030 S33: 0.0100 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 237 REMARK 3 ORIGIN FOR THE GROUP (A): 11.3710 -2.3252 12.2061 REMARK 3 T TENSOR REMARK 3 T11: 0.1125 T22: 0.1210 REMARK 3 T33: 0.0948 T12: -0.0095 REMARK 3 T13: 0.0337 T23: -0.0159 REMARK 3 L TENSOR REMARK 3 L11: 0.7598 L22: 1.0849 REMARK 3 L33: 0.8719 L12: -0.2180 REMARK 3 L13: 0.0299 L23: -0.9433 REMARK 3 S TENSOR REMARK 3 S11: 0.0161 S12: -0.0742 S13: 0.1091 REMARK 3 S21: -0.1999 S22: -0.1368 S23: -0.1352 REMARK 3 S31: 0.1712 S32: 0.1170 S33: 0.1207 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 238 A 309 REMARK 3 ORIGIN FOR THE GROUP (A): 15.7478 19.5513 -2.9908 REMARK 3 T TENSOR REMARK 3 T11: 0.1321 T22: 0.1462 REMARK 3 T33: 0.2010 T12: 0.0369 REMARK 3 T13: 0.0505 T23: 0.0478 REMARK 3 L TENSOR REMARK 3 L11: 0.0175 L22: 1.1869 REMARK 3 L33: 0.7180 L12: -0.0415 REMARK 3 L13: -0.0723 L23: -0.0545 REMARK 3 S TENSOR REMARK 3 S11: 0.0390 S12: 0.0014 S13: -0.0082 REMARK 3 S21: -0.2718 S22: -0.2683 S23: -0.4025 REMARK 3 S31: -0.1262 S32: -0.1276 S33: 0.2293 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 310 A 363 REMARK 3 ORIGIN FOR THE GROUP (A): 16.0910 25.6089 1.7722 REMARK 3 T TENSOR REMARK 3 T11: 0.1529 T22: 0.1020 REMARK 3 T33: 0.2424 T12: 0.0181 REMARK 3 T13: -0.0490 T23: 0.0863 REMARK 3 L TENSOR REMARK 3 L11: 0.3194 L22: 1.8505 REMARK 3 L33: 3.1038 L12: 0.6239 REMARK 3 L13: 0.7535 L23: 0.5684 REMARK 3 S TENSOR REMARK 3 S11: -0.1223 S12: -0.1340 S13: -0.0519 REMARK 3 S21: -0.1875 S22: -0.3363 S23: -0.4826 REMARK 3 S31: -0.6406 S32: -0.1132 S33: 0.4586 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 364 A 399 REMARK 3 ORIGIN FOR THE GROUP (A): 20.1499 15.1467 -2.4541 REMARK 3 T TENSOR REMARK 3 T11: 0.1413 T22: 0.1828 REMARK 3 T33: 0.3051 T12: 0.0954 REMARK 3 T13: 0.0449 T23: 0.1795 REMARK 3 L TENSOR REMARK 3 L11: 0.3004 L22: 2.6579 REMARK 3 L33: 1.3818 L12: 0.1596 REMARK 3 L13: -0.6403 L23: -0.5163 REMARK 3 S TENSOR REMARK 3 S11: 0.0273 S12: -0.1818 S13: -0.1738 REMARK 3 S21: -0.6036 S22: -0.4738 S23: -0.3155 REMARK 3 S31: 0.0467 S32: 0.4217 S33: 0.4464 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 400 A 535 REMARK 3 ORIGIN FOR THE GROUP (A): -9.5933 -12.8031 23.3773 REMARK 3 T TENSOR REMARK 3 T11: 0.1142 T22: 0.1117 REMARK 3 T33: 0.0806 T12: -0.0454 REMARK 3 T13: 0.0048 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 0.3604 L22: 0.1890 REMARK 3 L33: 0.1985 L12: 0.0534 REMARK 3 L13: -0.1663 L23: -0.0549 REMARK 3 S TENSOR REMARK 3 S11: -0.0555 S12: 0.0087 S13: -0.0811 REMARK 3 S21: -0.1176 S22: -0.0104 S23: -0.0389 REMARK 3 S31: 0.0487 S32: -0.0145 S33: 0.0659 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 536 A 567 REMARK 3 ORIGIN FOR THE GROUP (A): -17.1034 -29.3683 15.9626 REMARK 3 T TENSOR REMARK 3 T11: 0.1370 T22: 0.1357 REMARK 3 T33: 0.1878 T12: -0.0528 REMARK 3 T13: 0.0406 T23: -0.1553 REMARK 3 L TENSOR REMARK 3 L11: 3.2396 L22: 3.1771 REMARK 3 L33: 1.3870 L12: 2.1046 REMARK 3 L13: -0.8083 L23: -0.1072 REMARK 3 S TENSOR REMARK 3 S11: -0.2161 S12: 0.5412 S13: -0.6937 REMARK 3 S21: -0.2261 S22: 0.1691 S23: -0.3029 REMARK 3 S31: 0.1656 S32: -0.0622 S33: 0.0470 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 5ZNJ 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_1300007323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-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) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62796 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 57.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32 - 40% (V/V) PENTAERYTHRITOL REMARK 280 PROPOXYLATE (5/4 PO/OH), 0.1 - 0.2 M KCL AND 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 65.06950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.76750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 65.06950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.76750 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: 7970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 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 -12.07191 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 73.23775 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 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 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 CG CD OE1 OE2 REMARK 470 ILE A 255 CG1 CG2 CD1 REMARK 470 GLU A 256 CG CD OE1 OE2 REMARK 470 LYS A 261 CG CD CE NZ REMARK 470 MET A 281 CG SD CE REMARK 470 ASN A 313 OD1 ND2 REMARK 470 GLU A 315 CD OE1 OE2 REMARK 470 GLN A 319 CG CD OE1 NE2 REMARK 470 ASN A 324 CG OD1 ND2 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 CG CD CE NZ REMARK 470 ASP A 378 OD1 OD2 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 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 109 167.51 174.04 REMARK 500 GLU A 361 119.53 -160.99 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 ANP A 601 O2G REMARK 620 2 ANP A 601 O2B 91.4 REMARK 620 3 HOH A 718 O 92.4 94.7 REMARK 620 4 HOH A 767 O 88.7 175.3 89.9 REMARK 620 5 HOH A 794 O 175.2 91.4 91.3 88.2 REMARK 620 6 HOH A 912 O 92.9 89.3 173.3 86.1 83.3 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 HFG 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 PO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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). THE AUTHOR CONFIRMED PRORS OF MRSA R3708 SHOWS THR REMARK 999 230, ALA 278. DBREF1 5ZNJ A 1 567 UNP A0A227M497_STAAU DBREF2 5ZNJ A A0A227M497 1 567 SEQADV 5ZNJ THR A 230 UNP A0A227M49 ALA 230 SEE SEQUENCE DETAILS SEQADV 5ZNJ 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 HFG A 602 24 HET MG A 603 1 HET PO4 A 604 5 HET GOL A 605 6 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM HFG 7-BROMO-6-CHLORO-3-{3-[(2R,3S)-3-HYDROXYPIPERIDIN-2- HETNAM 2 HFG YL]-2-OXOPROPYL}QUINAZOLIN-4(3H)-ONE HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN HFG HALOFUGINONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 HFG C16 H17 BR CL N3 O3 FORMUL 4 MG MG 2+ FORMUL 5 PO4 O4 P 3- FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *273(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 MET A 421 1 7 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 GLY A 414 O MET A 437 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 ILE A 405 N ALA A 212 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 O2G ANP A 601 MG MG A 603 1555 1555 2.01 LINK O2B ANP A 601 MG MG A 603 1555 1555 1.99 LINK MG MG A 603 O HOH A 718 1555 1555 1.96 LINK MG MG A 603 O HOH A 767 1555 1555 2.10 LINK MG MG A 603 O HOH A 794 1555 1555 2.10 LINK MG MG A 603 O HOH A 912 1555 1555 2.31 CISPEP 1 LEU A 128 PRO A 129 0 4.55 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 HFG A 602 MG A 603 SITE 5 AC1 26 GOL A 605 HOH A 701 HOH A 711 HOH A 718 SITE 6 AC1 26 HOH A 733 HOH A 767 HOH A 794 HOH A 797 SITE 7 AC1 26 HOH A 821 HOH A 912 SITE 1 AC2 16 TRP A 80 ARG A 85 TYR A 89 GLU A 92 SITE 2 AC2 16 LEU A 93 PRO A 108 THR A 109 GLU A 111 SITE 3 AC2 16 ARG A 140 TYR A 161 GLN A 409 TYR A 440 SITE 4 AC2 16 GLY A 441 ANP A 601 HOH A 794 HOH A 796 SITE 1 AC3 6 ARG A 140 ANP A 601 HOH A 718 HOH A 767 SITE 2 AC3 6 HOH A 794 HOH A 912 SITE 1 AC4 3 GLY A 90 PRO A 91 GLU A 92 SITE 1 AC5 5 GLU A 209 ASP A 219 GLU A 406 ANP A 601 SITE 2 AC5 5 HOH A 701 CRYST1 130.139 77.535 74.226 90.00 99.36 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 0.007684 0.000000 0.001267 0.00000 SCALE2 0.000000 0.012897 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013654 0.00000