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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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