HEADER TRANSFERASE 26-AUG-15 5DF9
TITLE CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 IN COMPLEX WITH
TITLE 2 DEACYLATED PRODUCT OF CEFOPERAZONE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CELL DIVISION PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 35-579;
COMPND 5 SYNONYM: PENICILLIN-BINDING PROTEIN 3,PSEUDOMONAS AERUGINOSA GENOME
COMPND 6 ASSEMBLY PAE221;
COMPND 7 EC: 2.4.1.129;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA;
SOURCE 3 ORGANISM_TAXID: 287;
SOURCE 4 GENE: PBPB, FTSI_2, ERS445055_04698, PAE221_03076, YQ19_27590;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008
KEYWDS CEFOPERAZONE, BETA-LACTAM ANTIBIOTICS, ACYL-ENZYME COMPLEX, DE-
KEYWDS 2 ACYLATION, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.REN,J.E.NETTLESHIP,A.MALES,D.I.STUART,R.J.OWENS
REVDAT 3 10-JAN-24 5DF9 1 REMARK
REVDAT 2 10-FEB-16 5DF9 1 JRNL
REVDAT 1 13-JAN-16 5DF9 0
JRNL AUTH J.REN,J.E.NETTLESHIP,A.MALES,D.I.STUART,R.J.OWENS
JRNL TITL CRYSTAL STRUCTURES OF PENICILLIN-BINDING PROTEIN 3 IN
JRNL TITL 2 COMPLEXES WITH AZLOCILLIN AND CEFOPERAZONE IN BOTH ACYLATED
JRNL TITL 3 AND DEACYLATED FORMS.
JRNL REF FEBS LETT. V. 590 288 2016
JRNL REFN ISSN 0014-5793
JRNL PMID 26823174
JRNL DOI 10.1002/1873-3468.12054
REMARK 2
REMARK 2 RESOLUTION. 2.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0032
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.97
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 15029
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) : 0.205
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.249
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 786
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) : 2.70
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1110
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.49
REMARK 3 BIN R VALUE (WORKING SET) : 0.3290
REMARK 3 BIN FREE R VALUE SET COUNT : 57
REMARK 3 BIN FREE R VALUE : 0.4040
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3886
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 54
REMARK 3 SOLVENT ATOMS : 21
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.16
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -4.43000
REMARK 3 B22 (A**2) : -3.26000
REMARK 3 B33 (A**2) : 4.41000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 1.75000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.352
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.287
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.791
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4016 ; 0.004 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3919 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5451 ; 0.903 ; 1.982
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8982 ; 0.669 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 508 ; 4.858 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;32.469 ;23.136
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 660 ;12.857 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;11.152 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.049 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4570 ; 0.003 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 907 ; 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): 2035 ; 2.987 ;13.385
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2034 ; 2.978 ;13.385
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2542 ; 4.667 ;22.586
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2543 ; 4.667 ;22.588
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1981 ; 3.664 ;15.059
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1981 ; 3.662 ;15.058
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2910 ; 5.892 ;24.826
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4351 ; 8.339 ;61.074
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4349 ; 8.337 ;61.069
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 : 3
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 150
REMARK 3 ORIGIN FOR THE GROUP (A): 5.5516 18.8449 -16.3232
REMARK 3 T TENSOR
REMARK 3 T11: 0.0642 T22: 0.1792
REMARK 3 T33: 0.5081 T12: 0.0195
REMARK 3 T13: -0.0723 T23: -0.0178
REMARK 3 L TENSOR
REMARK 3 L11: 6.4255 L22: 0.8378
REMARK 3 L33: 0.8599 L12: 2.2057
REMARK 3 L13: -1.1870 L23: -0.1894
REMARK 3 S TENSOR
REMARK 3 S11: 0.3758 S12: -0.0516 S13: -0.2908
REMARK 3 S21: 0.1650 S22: -0.0335 S23: -0.2583
REMARK 3 S31: 0.0056 S32: -0.1295 S33: -0.3423
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 151 A 265
REMARK 3 ORIGIN FOR THE GROUP (A): -16.0134 9.9983 -15.3800
REMARK 3 T TENSOR
REMARK 3 T11: 0.2375 T22: 0.2742
REMARK 3 T33: 0.1204 T12: -0.0345
REMARK 3 T13: 0.0296 T23: 0.0466
REMARK 3 L TENSOR
REMARK 3 L11: 2.6593 L22: 1.5440
REMARK 3 L33: 0.8501 L12: 1.8584
REMARK 3 L13: 1.3852 L23: 1.1199
REMARK 3 S TENSOR
REMARK 3 S11: -0.0175 S12: -0.0513 S13: 0.2069
REMARK 3 S21: 0.0241 S22: -0.0271 S23: 0.0067
REMARK 3 S31: 0.0536 S32: 0.0633 S33: 0.0446
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 266 A 561
REMARK 3 ORIGIN FOR THE GROUP (A): -42.7221 -4.0207 -27.6867
REMARK 3 T TENSOR
REMARK 3 T11: 0.1858 T22: 0.1357
REMARK 3 T33: 0.2087 T12: -0.0220
REMARK 3 T13: 0.0295 T23: -0.0450
REMARK 3 L TENSOR
REMARK 3 L11: 2.3846 L22: 0.8364
REMARK 3 L33: 0.5500 L12: 0.4021
REMARK 3 L13: 0.7337 L23: 0.4999
REMARK 3 S TENSOR
REMARK 3 S11: 0.0300 S12: 0.1171 S13: -0.0387
REMARK 3 S21: 0.0060 S22: -0.1629 S23: 0.2832
REMARK 3 S31: -0.0313 S32: 0.0588 S33: 0.1329
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
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 5DF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-AUG-15.
REMARK 100 THE DEPOSITION ID IS D_1000213118.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 24-JAN-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 9.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I02
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15866
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : 0.09200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : 0.72200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900
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: 5DF8
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.10
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.26 M (NH4)2SO4; 0.1 M CHES PH 9.5;
REMARK 280 0.2 M NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
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 88.44200
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.63200
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 88.44200
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.63200
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 600 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 23170 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 16
REMARK 465 ALA A 17
REMARK 465 HIS A 18
REMARK 465 HIS A 19
REMARK 465 HIS A 20
REMARK 465 HIS A 21
REMARK 465 HIS A 22
REMARK 465 HIS A 23
REMARK 465 SER A 24
REMARK 465 SER A 25
REMARK 465 GLY A 26
REMARK 465 LEU A 27
REMARK 465 GLU A 28
REMARK 465 VAL A 29
REMARK 465 LEU A 30
REMARK 465 PHE A 31
REMARK 465 GLN A 32
REMARK 465 GLY A 33
REMARK 465 PRO A 34
REMARK 465 ASP A 35
REMARK 465 LEU A 36
REMARK 465 HIS A 37
REMARK 465 VAL A 38
REMARK 465 ILE A 39
REMARK 465 ASP A 40
REMARK 465 HIS A 41
REMARK 465 ASP A 42
REMARK 465 PHE A 43
REMARK 465 LEU A 44
REMARK 465 LYS A 45
REMARK 465 GLY A 46
REMARK 465 GLN A 47
REMARK 465 GLY A 48
REMARK 465 ASP A 49
REMARK 465 ALA A 50
REMARK 465 ARG A 51
REMARK 465 SER A 52
REMARK 465 THR A 562
REMARK 465 ALA A 563
REMARK 465 THR A 564
REMARK 465 GLU A 565
REMARK 465 GLN A 566
REMARK 465 GLN A 567
REMARK 465 GLN A 568
REMARK 465 VAL A 569
REMARK 465 ASN A 570
REMARK 465 ALA A 571
REMARK 465 ALA A 572
REMARK 465 PRO A 573
REMARK 465 ALA A 574
REMARK 465 LYS A 575
REMARK 465 GLY A 576
REMARK 465 GLY A 577
REMARK 465 ARG A 578
REMARK 465 GLY A 579
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 LYS A 141 16.81 56.67
REMARK 500 ASP A 169 -169.84 -77.02
REMARK 500 ASP A 198 -162.14 -115.40
REMARK 500 THR A 267 -169.61 -123.49
REMARK 500 ASN A 275 94.62 53.23
REMARK 500 PRO A 320 30.59 -95.83
REMARK 500 ARG A 395 -70.42 71.70
REMARK 500 ASN A 427 41.74 -93.16
REMARK 500 VAL A 493 83.90 -65.77
REMARK 500 ASP A 515 83.66 -158.41
REMARK 500 LYS A 529 16.60 -156.52
REMARK 500 ALA A 530 56.27 -166.13
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 59J 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 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5DF8 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS
REMARK 900 AERUGINOSA IN COMPLEX WITH CEFOPERAZONE
DBREF 5DF9 A 35 579 UNP Q51504 Q51504_PSEAI 35 579
SEQADV 5DF9 MET A 16 UNP Q51504 INITIATING METHIONINE
SEQADV 5DF9 ALA A 17 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 HIS A 18 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 HIS A 19 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 HIS A 20 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 HIS A 21 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 HIS A 22 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 HIS A 23 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 SER A 24 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 SER A 25 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 GLY A 26 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 LEU A 27 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 GLU A 28 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 VAL A 29 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 LEU A 30 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 PHE A 31 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 GLN A 32 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 GLY A 33 UNP Q51504 EXPRESSION TAG
SEQADV 5DF9 PRO A 34 UNP Q51504 EXPRESSION TAG
SEQRES 1 A 564 MET ALA HIS HIS HIS HIS HIS HIS SER SER GLY LEU GLU
SEQRES 2 A 564 VAL LEU PHE GLN GLY PRO ASP LEU HIS VAL ILE ASP HIS
SEQRES 3 A 564 ASP PHE LEU LYS GLY GLN GLY ASP ALA ARG SER VAL ARG
SEQRES 4 A 564 HIS ILE ALA ILE PRO ALA HIS ARG GLY LEU ILE THR ASP
SEQRES 5 A 564 ARG ASN GLY GLU PRO LEU ALA VAL SER THR PRO VAL THR
SEQRES 6 A 564 THR LEU TRP ALA ASN PRO LYS GLU LEU MET THR ALA LYS
SEQRES 7 A 564 GLU ARG TRP PRO GLN LEU ALA ALA ALA LEU GLY GLN ASP
SEQRES 8 A 564 THR LYS LEU PHE ALA ASP ARG ILE GLU GLN ASN ALA GLU
SEQRES 9 A 564 ARG GLU PHE ILE TYR LEU VAL ARG GLY LEU THR PRO GLU
SEQRES 10 A 564 GLN GLY GLU GLY VAL ILE ALA LEU LYS VAL PRO GLY VAL
SEQRES 11 A 564 TYR SER ILE GLU GLU PHE ARG ARG PHE TYR PRO ALA GLY
SEQRES 12 A 564 GLU VAL VAL ALA HIS ALA VAL GLY PHE THR ASP VAL ASP
SEQRES 13 A 564 ASP ARG GLY ARG GLU GLY ILE GLU LEU ALA PHE ASP GLU
SEQRES 14 A 564 TRP LEU ALA GLY VAL PRO GLY LYS ARG GLN VAL LEU LYS
SEQRES 15 A 564 ASP ARG ARG GLY ARG VAL ILE LYS ASP VAL GLN VAL THR
SEQRES 16 A 564 LYS ASN ALA LYS PRO GLY LYS THR LEU ALA LEU SER ILE
SEQRES 17 A 564 ASP LEU ARG LEU GLN TYR LEU ALA HIS ARG GLU LEU ARG
SEQRES 18 A 564 ASN ALA LEU LEU GLU ASN GLY ALA LYS ALA GLY SER LEU
SEQRES 19 A 564 VAL ILE MET ASP VAL LYS THR GLY GLU ILE LEU ALA MET
SEQRES 20 A 564 THR ASN GLN PRO THR TYR ASN PRO ASN ASN ARG ARG ASN
SEQRES 21 A 564 LEU GLN PRO ALA ALA MET ARG ASN ARG ALA MET ILE ASP
SEQRES 22 A 564 VAL PHE GLU PRO GLY SER THR VAL LYS PRO PHE SER MET
SEQRES 23 A 564 SER ALA ALA LEU ALA SER GLY ARG TRP LYS PRO SER ASP
SEQRES 24 A 564 ILE VAL ASP VAL TYR PRO GLY THR LEU GLN ILE GLY ARG
SEQRES 25 A 564 TYR THR ILE ARG ASP VAL SER ARG ASN SER ARG GLN LEU
SEQRES 26 A 564 ASP LEU THR GLY ILE LEU ILE LYS SER SER ASN VAL GLY
SEQRES 27 A 564 ILE SER LYS ILE ALA PHE ASP ILE GLY ALA GLU SER ILE
SEQRES 28 A 564 TYR SER VAL MET GLN GLN VAL GLY LEU GLY GLN ASP THR
SEQRES 29 A 564 GLY LEU GLY PHE PRO GLY GLU ARG VAL GLY ASN LEU PRO
SEQRES 30 A 564 ASN HIS ARG LYS TRP PRO LYS ALA GLU THR ALA THR LEU
SEQRES 31 A 564 ALA TYR GLY TYR GLY LEU SER VAL THR ALA ILE GLN LEU
SEQRES 32 A 564 ALA HIS ALA TYR ALA ALA LEU ALA ASN ASP GLY LYS SER
SEQRES 33 A 564 VAL PRO LEU SER MET THR ARG VAL ASP ARG VAL PRO ASP
SEQRES 34 A 564 GLY VAL GLN VAL ILE SER PRO GLU VAL ALA SER THR VAL
SEQRES 35 A 564 GLN GLY MET LEU GLN GLN VAL VAL GLU ALA GLN GLY GLY
SEQRES 36 A 564 VAL PHE ARG ALA GLN VAL PRO GLY TYR HIS ALA ALA GLY
SEQRES 37 A 564 LYS SER GLY THR ALA ARG LYS VAL SER VAL GLY THR LYS
SEQRES 38 A 564 GLY TYR ARG GLU ASN ALA TYR ARG SER LEU PHE ALA GLY
SEQRES 39 A 564 PHE ALA PRO ALA THR ASP PRO ARG ILE ALA MET VAL VAL
SEQRES 40 A 564 VAL ILE ASP GLU PRO SER LYS ALA GLY TYR PHE GLY GLY
SEQRES 41 A 564 LEU VAL SER ALA PRO VAL PHE SER LYS VAL MET ALA GLY
SEQRES 42 A 564 ALA LEU ARG LEU MET ASN VAL PRO PRO ASP ASN LEU PRO
SEQRES 43 A 564 THR ALA THR GLU GLN GLN GLN VAL ASN ALA ALA PRO ALA
SEQRES 44 A 564 LYS GLY GLY ARG GLY
HET SO4 A 601 5
HET SO4 A 602 5
HET 59J A 603 38
HET GOL A 604 6
HETNAM SO4 SULFATE ION
HETNAM 59J (2R,5R)-2-[(R)-CARBOXY{[(2R)-2-{[(4-ETHYL-2,3-
HETNAM 2 59J DIOXOPIPERAZIN-1-YL)CARBONYL]AMINO}-2-(4-
HETNAM 3 59J HYDROXYPHENYL)ACETYL]AMINO}METHYL]-5-METHYL-5,6-
HETNAM 4 59J DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 SO4 2(O4 S 2-)
FORMUL 4 59J C23 H27 N5 O9 S
FORMUL 5 GOL C3 H8 O3
FORMUL 6 HOH *21(H2 O)
HELIX 1 AA1 ASN A 85 MET A 90 1 6
HELIX 2 AA2 THR A 91 GLU A 94 5 4
HELIX 3 AA3 ARG A 95 LEU A 103 1 9
HELIX 4 AA4 ASP A 106 ASN A 117 1 12
HELIX 5 AA5 THR A 130 ALA A 139 1 10
HELIX 6 AA6 ALA A 157 VAL A 160 5 4
HELIX 7 AA7 VAL A 161 GLY A 166 1 6
HELIX 8 AA8 GLU A 176 PHE A 182 1 7
HELIX 9 AA9 PHE A 182 ALA A 187 1 6
HELIX 10 AB1 ASP A 224 ASN A 242 1 19
HELIX 11 AB2 PRO A 278 ARG A 282 5 5
HELIX 12 AB3 ASN A 283 ASP A 288 1 6
HELIX 13 AB4 PRO A 292 THR A 295 5 4
HELIX 14 AB5 VAL A 296 SER A 307 1 12
HELIX 15 AB6 LEU A 342 LYS A 348 1 7
HELIX 16 AB7 SER A 350 GLY A 362 1 13
HELIX 17 AB8 GLY A 362 VAL A 373 1 12
HELIX 18 AB9 PRO A 398 TYR A 407 1 10
HELIX 19 AC1 THR A 414 ASN A 427 1 14
HELIX 20 AC2 SER A 450 ALA A 467 1 18
HELIX 21 AC3 VAL A 471 GLN A 475 5 5
HELIX 22 AC4 PHE A 533 SER A 538 1 6
HELIX 23 AC5 SER A 538 MET A 553 1 16
SHEET 1 AA1 3 ARG A 54 ILE A 58 0
SHEET 2 AA1 3 GLY A 191 VAL A 195 -1 O VAL A 195 N ARG A 54
SHEET 3 AA1 3 VAL A 209 LYS A 211 -1 O LYS A 211 N LYS A 192
SHEET 1 AA2 3 ILE A 123 LEU A 129 0
SHEET 2 AA2 3 PRO A 72 ALA A 84 -1 N THR A 80 O LEU A 129
SHEET 3 AA2 3 VAL A 145 PHE A 154 -1 O GLU A 150 N VAL A 79
SHEET 1 AA3 4 ILE A 123 LEU A 129 0
SHEET 2 AA3 4 PRO A 72 ALA A 84 -1 N THR A 80 O LEU A 129
SHEET 3 AA3 4 ILE A 65 THR A 66 -1 N ILE A 65 O LEU A 73
SHEET 4 AA3 4 LEU A 219 ALA A 220 1 O LEU A 219 N THR A 66
SHEET 1 AA4 2 GLY A 188 VAL A 189 0
SHEET 2 AA4 2 LYS A 214 PRO A 215 -1 O LYS A 214 N VAL A 189
SHEET 1 AA5 5 ILE A 259 GLN A 265 0
SHEET 2 AA5 5 ALA A 246 ASP A 253 -1 N ILE A 251 O ALA A 261
SHEET 3 AA5 5 ILE A 518 ASP A 525 -1 O ASP A 525 N ALA A 246
SHEET 4 AA5 5 TYR A 498 ALA A 511 -1 N GLY A 509 O MET A 520
SHEET 5 AA5 5 ALA A 482 VAL A 491 -1 N LYS A 484 O ALA A 508
SHEET 1 AA6 2 ILE A 315 ASP A 317 0
SHEET 2 AA6 2 GLN A 339 ASP A 341 -1 O LEU A 340 N VAL A 316
SHEET 1 AA7 2 THR A 322 ILE A 325 0
SHEET 2 AA7 2 TYR A 328 ARG A 331 -1 O TYR A 328 N ILE A 325
SHEET 1 AA8 2 LYS A 430 SER A 431 0
SHEET 2 AA8 2 VAL A 446 GLN A 447 -1 O VAL A 446 N SER A 431
CISPEP 1 GLN A 265 PRO A 266 0 2.62
CISPEP 2 TYR A 319 PRO A 320 0 -1.38
CISPEP 3 ALA A 511 PRO A 512 0 -6.26
CISPEP 4 LEU A 560 PRO A 561 0 -7.70
SITE 1 AC1 3 ARG A 387 VAL A 388 GLY A 389
SITE 1 AC2 2 LYS A 490 LYS A 529
SITE 1 AC3 18 ASN A 275 SER A 294 VAL A 333 SER A 349
SITE 2 AC3 18 ASN A 351 THR A 404 TYR A 407 TYR A 409
SITE 3 AC3 18 SER A 485 GLY A 486 THR A 487 ARG A 489
SITE 4 AC3 18 TYR A 498 TYR A 503 TYR A 532 PHE A 533
SITE 5 AC3 18 GLY A 534 GLY A 535
SITE 1 AC4 5 GLY A 247 SER A 248 ARG A 284 PHE A 290
SITE 2 AC4 5 ASP A 525
CRYST1 176.884 41.264 87.786 90.00 117.42 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 0.005653 0.000000 0.002933 0.00000
SCALE2 0.000000 0.024234 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012833 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
