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