HEADER HYDROLASE/ANTIBIOTIC 01-MAY-12 4EYB TITLE CRYSTAL STRUCTURE OF NDM-1 BOUND TO HYDROLYZED OXACILLIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE NDM-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NDM-1, METALLO-BETA-LACTAMASE NDM-1; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLANDM-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METALLO BETA LACTAMASE, ANTIBIOTIC, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.C.J.STRYNADKA,D.T.KING REVDAT 3 28-FEB-24 4EYB 1 COMPND REMARK HETNAM LINK REVDAT 2 15-NOV-17 4EYB 1 REMARK REVDAT 1 15-AUG-12 4EYB 0 JRNL AUTH D.T.KING,L.J.WORRALL,R.GRUNINGER,N.C.STRYNADKA JRNL TITL NEW DELHI METALLO-BETA-LACTAMASE: STRUCTURAL INSIGHTS INTO JRNL TITL 2 BETA-LACTAM RECOGNITION AND INHIBITION JRNL REF J.AM.CHEM.SOC. V. 134 11362 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22713171 JRNL DOI 10.1021/JA303579D REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 135810 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) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7157 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) : 1.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9824 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 495 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3594 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 405 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.62000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : -0.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.034 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.965 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3755 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5125 ; 2.143 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 486 ; 6.328 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;32.263 ;24.534 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 556 ;12.807 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.739 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 571 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2916 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2395 ; 2.949 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3820 ; 4.327 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1360 ; 6.005 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1302 ; 8.674 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3755 ; 2.877 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4EYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072221. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : TOROIDAL FOCUSING MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 143064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 25.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MGCL2, 25% PEG3350, 0.1M BIS REMARK 280 -TRIS, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.60000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.07500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.68500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.07500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.60000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.68500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: IT IS UNCERTAIN WHETHER THE BIOLOGICALLY ACTIVE FORM IS REMARK 300 MONOMERIC OR DIMERIC 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 39.68500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 67.07500 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 1 REMARK 465 GLU A 2 REMARK 465 LEU A 3 REMARK 465 PRO A 4 REMARK 465 ASN A 5 REMARK 465 ILE A 6 REMARK 465 MET A 7 REMARK 465 HIS A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 LYS A 12 REMARK 465 LEU A 13 REMARK 465 SER A 14 REMARK 465 THR A 15 REMARK 465 ALA A 16 REMARK 465 LEU A 17 REMARK 465 ALA A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 LEU A 21 REMARK 465 MET A 22 REMARK 465 LEU A 23 REMARK 465 SER A 24 REMARK 465 GLY A 25 REMARK 465 CYS A 26 REMARK 465 MET A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 LEU B 3 REMARK 465 PRO B 4 REMARK 465 ASN B 5 REMARK 465 ILE B 6 REMARK 465 MET B 7 REMARK 465 HIS B 8 REMARK 465 PRO B 9 REMARK 465 VAL B 10 REMARK 465 ALA B 11 REMARK 465 LYS B 12 REMARK 465 LEU B 13 REMARK 465 SER B 14 REMARK 465 THR B 15 REMARK 465 ALA B 16 REMARK 465 LEU B 17 REMARK 465 ALA B 18 REMARK 465 ALA B 19 REMARK 465 ALA B 20 REMARK 465 LEU B 21 REMARK 465 MET B 22 REMARK 465 LEU B 23 REMARK 465 SER B 24 REMARK 465 GLY B 25 REMARK 465 CYS B 26 REMARK 465 MET B 27 REMARK 465 PRO B 28 REMARK 465 GLY B 29 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 512 O HOH A 513 1.86 REMARK 500 O HOH A 513 O HOH A 575 1.86 REMARK 500 O HOH A 543 O HOH A 609 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 43 CB - CG - OD1 ANGL. DEV. = 9.3 DEGREES REMARK 500 ASP A 90 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP A 130 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 LYS A 211 CG - CD - CE ANGL. DEV. = 19.6 DEGREES REMARK 500 LYS A 211 CD - CE - NZ ANGL. DEV. = 20.0 DEGREES REMARK 500 ARG A 264 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 85 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 85 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 PHE B 177 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 70 -34.66 -133.17 REMARK 500 ASP A 90 140.43 75.91 REMARK 500 PHE B 70 -39.29 -132.34 REMARK 500 ASP B 90 142.24 72.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE STARTING MATERIAL USED FOR CRYSTALLIZATION CORRESPOND TO THE REMARK 600 UNREACTED FORM OF OXACILLIN 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 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 98.2 REMARK 620 3 HIS A 189 NE2 98.3 122.3 REMARK 620 4 0WO A 303 O 173.3 84.7 85.1 REMARK 620 5 HOH A 598 O 90.2 123.3 111.4 83.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 95.8 REMARK 620 3 HIS A 250 NE2 88.5 110.2 REMARK 620 4 0WO A 303 NAP 94.5 131.4 117.4 REMARK 620 5 0WO A 303 OAH 168.5 95.5 89.9 76.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 98.7 REMARK 620 3 HIS B 189 NE2 98.2 123.5 REMARK 620 4 0WO B 301 O 174.4 84.8 83.3 REMARK 620 5 HOH B 558 O 90.6 123.0 110.3 83.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 95.0 REMARK 620 3 HIS B 250 NE2 89.2 110.9 REMARK 620 4 0WO B 301 NAP 93.8 131.7 116.6 REMARK 620 5 0WO B 301 OAH 167.7 96.2 91.4 74.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 152 OE2 REMARK 620 2 GLU B 152 OE1 49.7 REMARK 620 3 ASP B 223 OD2 112.3 101.2 REMARK 620 4 HOH B 562 O 122.2 78.9 100.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0WO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0WO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q6X RELATED DB: PDB REMARK 900 RELATED ID: 3SPU RELATED DB: PDB REMARK 900 RELATED ID: 4EXS RELATED DB: PDB REMARK 900 RELATED ID: 4EXY RELATED DB: PDB REMARK 900 RELATED ID: 4EY2 RELATED DB: PDB REMARK 900 RELATED ID: 4EYF RELATED DB: PDB REMARK 900 RELATED ID: 4EYL RELATED DB: PDB DBREF 4EYB A 1 270 UNP C7C422 BLAN1_KLEPN 1 270 DBREF 4EYB B 1 270 UNP C7C422 BLAN1_KLEPN 1 270 SEQRES 1 A 270 MET GLU LEU PRO ASN ILE MET HIS PRO VAL ALA LYS LEU SEQRES 2 A 270 SER THR ALA LEU ALA ALA ALA LEU MET LEU SER GLY CYS SEQRES 3 A 270 MET PRO GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET SEQRES 4 A 270 GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 5 A 270 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 6 A 270 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 7 A 270 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 8 A 270 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 9 A 270 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 10 A 270 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 11 A 270 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 12 A 270 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 13 A 270 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 14 A 270 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 15 A 270 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 16 A 270 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 17 A 270 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 18 A 270 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 19 A 270 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 20 A 270 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 21 A 270 HIS THR ALA ARG MET ALA ASP LYS LEU ARG SEQRES 1 B 270 MET GLU LEU PRO ASN ILE MET HIS PRO VAL ALA LYS LEU SEQRES 2 B 270 SER THR ALA LEU ALA ALA ALA LEU MET LEU SER GLY CYS SEQRES 3 B 270 MET PRO GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET SEQRES 4 B 270 GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 5 B 270 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 6 B 270 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 7 B 270 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 8 B 270 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 9 B 270 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 10 B 270 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 11 B 270 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 12 B 270 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 13 B 270 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 14 B 270 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 15 B 270 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 16 B 270 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 17 B 270 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 18 B 270 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 19 B 270 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 20 B 270 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 21 B 270 HIS THR ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET 0WO A 303 29 HET 0WO B 301 29 HET ZN B 302 1 HET ZN B 303 1 HET ZN B 304 1 HETNAM ZN ZINC ION HETNAM 0WO (2R,4S)-2-[(R)-CARBOXY{[(5-METHYL-3-PHENYL-1,2-OXAZOL- HETNAM 2 0WO 4-YL)CARBONYL]AMINO}METHYL]-5,5-DIMETHYL-1,3- HETNAM 3 0WO THIAZOLIDINE-4-CARBO XYLIC ACID HETSYN 0WO OXACILLIN, HYDROXYLATED FORM FORMUL 3 ZN 5(ZN 2+) FORMUL 5 0WO 2(C19 H21 N3 O6 S) FORMUL 10 HOH *405(H2 O) HELIX 1 1 THR A 94 ILE A 109 1 16 HELIX 2 2 HIS A 122 GLY A 127 1 6 HELIX 3 3 GLY A 128 ALA A 135 1 8 HELIX 4 4 ALA A 143 ALA A 149 1 7 HELIX 5 5 PRO A 150 GLY A 153 5 4 HELIX 6 6 GLU A 170 ALA A 174 5 5 HELIX 7 7 HIS A 228 PHE A 240 1 13 HELIX 8 8 ARG A 256 LYS A 268 1 13 HELIX 9 9 THR B 94 ILE B 109 1 16 HELIX 10 10 HIS B 122 GLY B 127 1 6 HELIX 11 11 GLY B 128 ALA B 135 1 8 HELIX 12 12 ALA B 143 ALA B 149 1 7 HELIX 13 13 PRO B 150 GLY B 153 5 4 HELIX 14 14 GLU B 170 ALA B 174 5 5 HELIX 15 15 HIS B 228 PHE B 240 1 13 HELIX 16 16 ARG B 256 LYS B 268 1 13 SHEET 1 A 8 ASP A 43 PHE A 46 0 SHEET 2 A 8 LEU A 49 ALA A 55 -1 O PHE A 51 N GLN A 44 SHEET 3 A 8 VAL A 58 MET A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 A 8 GLY A 71 ASP A 82 -1 O ILE A 79 N TRP A 59 SHEET 5 A 8 ARG A 85 VAL A 89 -1 O ARG A 85 N ASP A 82 SHEET 6 A 8 VAL A 113 VAL A 117 1 O ALA A 114 N VAL A 86 SHEET 7 A 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 A 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 B 4 LEU A 180 PHE A 183 0 SHEET 2 B 4 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181 SHEET 3 B 4 ILE A 203 PHE A 205 -1 O PHE A 205 N VAL A 196 SHEET 4 B 4 MET A 245 VAL A 247 1 O VAL A 247 N ALA A 204 SHEET 1 C 8 ASP B 43 PHE B 46 0 SHEET 2 C 8 LEU B 49 ALA B 55 -1 O PHE B 51 N GLN B 44 SHEET 3 C 8 VAL B 58 MET B 67 -1 O GLN B 60 N ARG B 52 SHEET 4 C 8 GLY B 71 ASP B 82 -1 O ILE B 79 N TRP B 59 SHEET 5 C 8 ARG B 85 VAL B 89 -1 O LEU B 87 N VAL B 80 SHEET 6 C 8 VAL B 113 VAL B 117 1 O VAL B 117 N VAL B 88 SHEET 7 C 8 ALA B 138 ASN B 142 1 O TYR B 140 N ALA B 116 SHEET 8 C 8 HIS B 159 LEU B 161 1 O LEU B 161 N ALA B 141 SHEET 1 D 4 LEU B 180 PHE B 183 0 SHEET 2 D 4 THR B 195 ILE B 198 -1 O GLY B 197 N LYS B 181 SHEET 3 D 4 ILE B 203 PHE B 205 -1 O PHE B 205 N VAL B 196 SHEET 4 D 4 MET B 245 VAL B 247 1 O VAL B 247 N ALA B 204 LINK NE2 HIS A 120 ZN ZN A 302 1555 1555 2.14 LINK ND1 HIS A 122 ZN ZN A 302 1555 1555 1.93 LINK OD2 ASP A 124 ZN ZN A 301 1555 1555 2.13 LINK NE2 HIS A 189 ZN ZN A 302 1555 1555 2.00 LINK SG CYS A 208 ZN ZN A 301 1555 1555 2.38 LINK NE2 HIS A 250 ZN ZN A 301 1555 1555 1.99 LINK ZN ZN A 301 NAP 0WO A 303 1555 1555 2.12 LINK ZN ZN A 301 OAH 0WO A 303 1555 1555 2.16 LINK ZN ZN A 302 O 0WO A 303 1555 1555 2.45 LINK ZN ZN A 302 O HOH A 598 1555 1555 1.98 LINK NE2 HIS B 120 ZN ZN B 302 1555 1555 2.10 LINK ND1 HIS B 122 ZN ZN B 302 1555 1555 1.94 LINK OD2 ASP B 124 ZN ZN B 303 1555 1555 2.15 LINK OE2 GLU B 152 ZN ZN B 304 1555 1555 2.49 LINK OE1 GLU B 152 ZN ZN B 304 1555 1555 2.63 LINK NE2 HIS B 189 ZN ZN B 302 1555 1555 2.01 LINK SG CYS B 208 ZN ZN B 303 1555 1555 2.36 LINK OD2 ASP B 223 ZN ZN B 304 1555 1555 2.04 LINK NE2 HIS B 250 ZN ZN B 303 1555 1555 1.99 LINK O 0WO B 301 ZN ZN B 302 1555 1555 2.51 LINK NAP 0WO B 301 ZN ZN B 303 1555 1555 2.15 LINK OAH 0WO B 301 ZN ZN B 303 1555 1555 2.15 LINK ZN ZN B 302 O HOH B 558 1555 1555 1.96 LINK ZN ZN B 304 O HOH B 562 1555 1555 1.94 SITE 1 AC1 5 ASP A 124 CYS A 208 HIS A 250 0WO A 303 SITE 2 AC1 5 HOH A 598 SITE 1 AC2 5 HIS A 120 HIS A 122 HIS A 189 0WO A 303 SITE 2 AC2 5 HOH A 598 SITE 1 AC3 19 TRP A 93 HIS A 122 GLN A 123 ASP A 124 SITE 2 AC3 19 GLU A 152 MET A 154 HIS A 189 CYS A 208 SITE 3 AC3 19 LYS A 211 GLY A 219 ASN A 220 HIS A 250 SITE 4 AC3 19 ZN A 301 ZN A 302 HOH A 449 HOH A 534 SITE 5 AC3 19 HOH A 598 THR B 34 GLY B 69 SITE 1 AC4 19 THR A 34 GLY A 69 TRP B 93 HIS B 122 SITE 2 AC4 19 GLN B 123 ASP B 124 GLU B 152 MET B 154 SITE 3 AC4 19 HIS B 189 CYS B 208 LYS B 211 GLY B 219 SITE 4 AC4 19 ASN B 220 HIS B 250 ZN B 302 ZN B 303 SITE 5 AC4 19 HOH B 529 HOH B 558 HOH B 561 SITE 1 AC5 5 HIS B 120 HIS B 122 HIS B 189 0WO B 301 SITE 2 AC5 5 HOH B 558 SITE 1 AC6 5 ASP B 124 CYS B 208 HIS B 250 0WO B 301 SITE 2 AC6 5 HOH B 558 SITE 1 AC7 4 GLU A 227 GLU B 152 ASP B 223 HOH B 562 CRYST1 39.200 79.370 134.150 90.00 90.00 90.00 P 21 21 21 8 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 0.025510 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007454 0.00000