10 20 30 40 50 60 70 80 3BFF - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 21-NOV-07 3BFF
TITLE CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH FAROPENEM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS A BETA-LACTAMASE SED1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: SED-G238C, UNP RESIDUES 34-295; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CITROBACTER SEDLAKII; SOURCE 3 ORGANISM_TAXID: 67826; SOURCE 4 STRAIN: 2596; SOURCE 5 GENE: BLA-SED-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET29A
KEYWDS HYDROLASE, BETA-LACTAMASE, CLASS A SED-G238C, FAROPENEM, KEYWDS 2 ACYL-ENZYME
EXPDTA X-RAY DIFFRACTION
AUTHOR L.PERNOT,S.PETRELLA,W.SOUGAKOFF
REVDAT 2 24-FEB-09 3BFF 1 VERSN REVDAT 1 18-DEC-07 3BFF 0
JRNL AUTH L.PERNOT,S.PETRELLA,W.SOUGAKOFF JRNL TITL ACYL-INTERMEDIATE STRUCTURES OF THE CLASS A JRNL TITL 2 BETA-LACTAMASE SED-G238C JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.PETRELLA,L.PERNOT,W.SOUGAKOFF REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION REMARK 1 TITL 2 STUDY OF THE CLASS A BETA-LACTAMASE SED-1 AND ITS REMARK 1 TITL 3 MUTANT SED-G238C FROM CITROBACTER SEDLAKII REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 60 125 2004 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 14684905 REMARK 1 DOI 10.1107/S0907444903022765
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 87314 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 SET) : 0.180 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3651 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 14550 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 580 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7948 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 1133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.05000 REMARK 3 B22 (A**2) : -1.21000 REMARK 3 B33 (A**2) : 3.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.91 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 3BFF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-NOV-07. REMARK 100 THE RCSB ID CODE IS RCSB045452.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.984 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90973 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 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: PDB ENTRY 3BFD REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG MME 2000, 200MM KSCN, 100MM REMARK 280 SODIUM CACODYLATE PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K
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 93.55800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.62200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 93.55800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.62200 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, 4 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 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 CYS C 69 CA - CB - SG ANGL. DEV. = 9.4 DEGREES REMARK 500 CYS C 238 CA - CB - SG ANGL. DEV. = 8.8 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 CYS A 69 -137.08 56.52 REMARK 500 THR A 103 -144.58 -121.14 REMARK 500 SER A 220 -127.70 -101.73 REMARK 500 GLU A 254 -126.41 53.02 REMARK 500 CYS B 69 -137.33 55.68 REMARK 500 THR B 103 -146.15 -123.43 REMARK 500 LEU B 169 0.43 -68.23 REMARK 500 SER B 220 -129.43 -106.54 REMARK 500 ASP B 246 135.06 -172.27 REMARK 500 GLU B 254 -125.19 50.21 REMARK 500 CYS C 69 -137.37 55.52 REMARK 500 THR C 103 -152.01 -124.12 REMARK 500 SER C 220 -125.11 -104.30 REMARK 500 GLU C 254 -128.08 51.01 REMARK 500 CYS D 69 -138.00 52.64 REMARK 500 THR D 103 -143.02 -115.44 REMARK 500 SER D 220 -126.52 -102.40 REMARK 500 ASP D 246 132.12 -171.13 REMARK 500 GLU D 254 -127.54 52.93 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 771 DISTANCE = 5.44 ANGSTROMS REMARK 525 HOH A 595 DISTANCE = 6.92 ANGSTROMS
REMARK 600 REMARK 600 HETEROGEN REMARK 600 SFR IS THE HYDROLYZED FORM OF FPM, BOUND TO THE PROTEIN REMARK 600 VIA A COVALENT LINK WITH THE OG ATOM OF SER 70.
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN B 1 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 2 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN B 3 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN B 4 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN C 5 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN D 6 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FPM C 1 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFR A 301 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFR B 302 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFR C 303 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SFR D 304
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BFC RELATED DB: PDB REMARK 900 CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH IMIPENEM REMARK 900 RELATED ID: 3BFD RELATED DB: PDB REMARK 900 CLASS A BETA-LACTAMASE SED-G238C REMARK 900 RELATED ID: 3BFE RELATED DB: PDB REMARK 900 CLASS A BETA-LACTAMASE SED-1 REMARK 900 RELATED ID: 3BFG RELATED DB: PDB REMARK 900 CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH MEROPENEM
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. REMARK 999 THREE NUMBERS, 58, 239, AND 253 WERE SIMPLY SKIPPED IN THE REMARK 999 NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON REMARK 999 DENSITY.
DBREF 3BFF A 26 290 UNP Q93PQ0 Q93PQ0_9ENTR 34 295 DBREF 3BFF B 26 290 UNP Q93PQ0 Q93PQ0_9ENTR 34 295 DBREF 3BFF C 26 290 UNP Q93PQ0 Q93PQ0_9ENTR 34 295 DBREF 3BFF D 26 290 UNP Q93PQ0 Q93PQ0_9ENTR 34 295
SEQADV 3BFF CYS A 238 UNP Q93PQ0 GLY 245 ENGINEERED SEQADV 3BFF CYS B 238 UNP Q93PQ0 GLY 245 ENGINEERED SEQADV 3BFF CYS C 238 UNP Q93PQ0 GLY 245 ENGINEERED SEQADV 3BFF CYS D 238 UNP Q93PQ0 GLY 245 ENGINEERED
SEQRES 1 A 262 VAL GLN GLN VAL GLN LYS LYS LEU ALA ALA LEU GLU LYS SEQRES 2 A 262 GLN SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASN THR SEQRES 3 A 262 ALA ASP ASN SER GLN VAL LEU TYR ARG ALA ASP GLU ARG SEQRES 4 A 262 PHE ALA MET CYS SER THR SER LYS VAL MET THR ALA ALA SEQRES 5 A 262 ALA VAL LEU LYS GLN SER GLU THR HIS ASP GLY ILE LEU SEQRES 6 A 262 GLN GLN LYS MET THR ILE LYS LYS ALA ASP LEU THR ASN SEQRES 7 A 262 TRP ASN PRO VAL THR GLU LYS TYR VAL GLY ASN THR MET SEQRES 8 A 262 THR LEU ALA GLU LEU SER ALA ALA THR LEU GLN TYR SER SEQRES 9 A 262 ASP ASN THR ALA MET ASN LYS LEU LEU ALA HIS LEU GLY SEQRES 10 A 262 GLY PRO GLY ASN VAL THR ALA PHE ALA ARG SER ILE GLY SEQRES 11 A 262 ASP THR THR PHE ARG LEU ASP ARG LYS GLU PRO GLU LEU SEQRES 12 A 262 ASN THR ALA ILE PRO GLY ASP GLU ARG ASP THR THR SER SEQRES 13 A 262 PRO LEU ALA MET ALA LYS SER LEU ARG LYS LEU THR LEU SEQRES 14 A 262 GLY ASP ALA LEU ALA GLY PRO GLN ARG ALA GLN LEU VAL SEQRES 15 A 262 ASP TRP LEU LYS GLY ASN THR THR GLY GLY GLN SER ILE SEQRES 16 A 262 ARG ALA GLY LEU PRO ALA HIS TRP VAL VAL GLY ASP LYS SEQRES 17 A 262 THR GLY ALA CYS ASP TYR GLY THR THR ASN ASP ILE ALA SEQRES 18 A 262 VAL ILE TRP PRO GLU ASP ARG ALA PRO LEU VAL LEU VAL SEQRES 19 A 262 THR TYR PHE THR GLN PRO GLN GLN ASP ALA LYS TRP ARG SEQRES 20 A 262 LYS ASP VAL LEU ALA ALA ALA ALA LYS ILE VAL THR GLU SEQRES 21 A 262 GLY LYS SEQRES 1 B 262 VAL GLN GLN VAL GLN LYS LYS LEU ALA ALA LEU GLU LYS SEQRES 2 B 262 GLN SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASN THR SEQRES 3 B 262 ALA ASP ASN SER GLN VAL LEU TYR ARG ALA ASP GLU ARG SEQRES 4 B 262 PHE ALA MET CYS SER THR SER LYS VAL MET THR ALA ALA SEQRES 5 B 262 ALA VAL LEU LYS GLN SER GLU THR HIS ASP GLY ILE LEU SEQRES 6 B 262 GLN GLN LYS MET THR ILE LYS LYS ALA ASP LEU THR ASN SEQRES 7 B 262 TRP ASN PRO VAL THR GLU LYS TYR VAL GLY ASN THR MET SEQRES 8 B 262 THR LEU ALA GLU LEU SER ALA ALA THR LEU GLN TYR SER SEQRES 9 B 262 ASP ASN THR ALA MET ASN LYS LEU LEU ALA HIS LEU GLY SEQRES 10 B 262 GLY PRO GLY ASN VAL THR ALA PHE ALA ARG SER ILE GLY SEQRES 11 B 262 ASP THR THR PHE ARG LEU ASP ARG LYS GLU PRO GLU LEU SEQRES 12 B 262 ASN THR ALA ILE PRO GLY ASP GLU ARG ASP THR THR SER SEQRES 13 B 262 PRO LEU ALA MET ALA LYS SER LEU ARG LYS LEU THR LEU SEQRES 14 B 262 GLY ASP ALA LEU ALA GLY PRO GLN ARG ALA GLN LEU VAL SEQRES 15 B 262 ASP TRP LEU LYS GLY ASN THR THR GLY GLY GLN SER ILE SEQRES 16 B 262 ARG ALA GLY LEU PRO ALA HIS TRP VAL VAL GLY ASP LYS SEQRES 17 B 262 THR GLY ALA CYS ASP TYR GLY THR THR ASN ASP ILE ALA SEQRES 18 B 262 VAL ILE TRP PRO GLU ASP ARG ALA PRO LEU VAL LEU VAL SEQRES 19 B 262 THR TYR PHE THR GLN PRO GLN GLN ASP ALA LYS TRP ARG SEQRES 20 B 262 LYS ASP VAL LEU ALA ALA ALA ALA LYS ILE VAL THR GLU SEQRES 21 B 262 GLY LYS SEQRES 1 C 262 VAL GLN GLN VAL GLN LYS LYS LEU ALA ALA LEU GLU LYS SEQRES 2 C 262 GLN SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASN THR SEQRES 3 C 262 ALA ASP ASN SER GLN VAL LEU TYR ARG ALA ASP GLU ARG SEQRES 4 C 262 PHE ALA MET CYS SER THR SER LYS VAL MET THR ALA ALA SEQRES 5 C 262 ALA VAL LEU LYS GLN SER GLU THR HIS ASP GLY ILE LEU SEQRES 6 C 262 GLN GLN LYS MET THR ILE LYS LYS ALA ASP LEU THR ASN SEQRES 7 C 262 TRP ASN PRO VAL THR GLU LYS TYR VAL GLY ASN THR MET SEQRES 8 C 262 THR LEU ALA GLU LEU SER ALA ALA THR LEU GLN TYR SER SEQRES 9 C 262 ASP ASN THR ALA MET ASN LYS LEU LEU ALA HIS LEU GLY SEQRES 10 C 262 GLY PRO GLY ASN VAL THR ALA PHE ALA ARG SER ILE GLY SEQRES 11 C 262 ASP THR THR PHE ARG LEU ASP ARG LYS GLU PRO GLU LEU SEQRES 12 C 262 ASN THR ALA ILE PRO GLY ASP GLU ARG ASP THR THR SER SEQRES 13 C 262 PRO LEU ALA MET ALA LYS SER LEU ARG LYS LEU THR LEU SEQRES 14 C 262 GLY ASP ALA LEU ALA GLY PRO GLN ARG ALA GLN LEU VAL SEQRES 15 C 262 ASP TRP LEU LYS GLY ASN THR THR GLY GLY GLN SER ILE SEQRES 16 C 262 ARG ALA GLY LEU PRO ALA HIS TRP VAL VAL GLY ASP LYS SEQRES 17 C 262 THR GLY ALA CYS ASP TYR GLY THR THR ASN ASP ILE ALA SEQRES 18 C 262 VAL ILE TRP PRO GLU ASP ARG ALA PRO LEU VAL LEU VAL SEQRES 19 C 262 THR TYR PHE THR GLN PRO GLN GLN ASP ALA LYS TRP ARG SEQRES 20 C 262 LYS ASP VAL LEU ALA ALA ALA ALA LYS ILE VAL THR GLU SEQRES 21 C 262 GLY LYS SEQRES 1 D 262 VAL GLN GLN VAL GLN LYS LYS LEU ALA ALA LEU GLU LYS SEQRES 2 D 262 GLN SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASN THR SEQRES 3 D 262 ALA ASP ASN SER GLN VAL LEU TYR ARG ALA ASP GLU ARG SEQRES 4 D 262 PHE ALA MET CYS SER THR SER LYS VAL MET THR ALA ALA SEQRES 5 D 262 ALA VAL LEU LYS GLN SER GLU THR HIS ASP GLY ILE LEU SEQRES 6 D 262 GLN GLN LYS MET THR ILE LYS LYS ALA ASP LEU THR ASN SEQRES 7 D 262 TRP ASN PRO VAL THR GLU LYS TYR VAL GLY ASN THR MET SEQRES 8 D 262 THR LEU ALA GLU LEU SER ALA ALA THR LEU GLN TYR SER SEQRES 9 D 262 ASP ASN THR ALA MET ASN LYS LEU LEU ALA HIS LEU GLY SEQRES 10 D 262 GLY PRO GLY ASN VAL THR ALA PHE ALA ARG SER ILE GLY SEQRES 11 D 262 ASP THR THR PHE ARG LEU ASP ARG LYS GLU PRO GLU LEU SEQRES 12 D 262 ASN THR ALA ILE PRO GLY ASP GLU ARG ASP THR THR SER SEQRES 13 D 262 PRO LEU ALA MET ALA LYS SER LEU ARG LYS LEU THR LEU SEQRES 14 D 262 GLY ASP ALA LEU ALA GLY PRO GLN ARG ALA GLN LEU VAL SEQRES 15 D 262 ASP TRP LEU LYS GLY ASN THR THR GLY GLY GLN SER ILE SEQRES 16 D 262 ARG ALA GLY LEU PRO ALA HIS TRP VAL VAL GLY ASP LYS SEQRES 17 D 262 THR GLY ALA CYS ASP TYR GLY THR THR ASN ASP ILE ALA SEQRES 18 D 262 VAL ILE TRP PRO GLU ASP ARG ALA PRO LEU VAL LEU VAL SEQRES 19 D 262 THR TYR PHE THR GLN PRO GLN GLN ASP ALA LYS TRP ARG SEQRES 20 D 262 LYS ASP VAL LEU ALA ALA ALA ALA LYS ILE VAL THR GLU SEQRES 21 D 262 GLY LYS
HET SCN B 1 3 HET SCN A 2 3 HET SCN B 3 3 HET SCN B 4 3 HET SCN C 5 3 HET SCN D 6 3 HET FPM C 1 19 HET SFR A 301 19 HET SFR B 302 19 HET SFR C 303 19 HET SFR D 304 19
HETNAM SCN THIOCYANATE ION HETNAM FPM (5R,6S)-6-(1-HYDROXYETHYL)-7-OXO-3-[(2R)-OXOLAN-2-YL]- HETNAM 2 FPM 4-THIA-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2-CARBOXYLIC ACID HETNAM SFR (2R)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-5-[(2R)- HETNAM 2 SFR TETRAHYDROFURAN-2-YL]-2,3-DIHYDRO-1,3-THIAZOLE-4- HETNAM 3 SFR CARBOXYLIC ACID
HETSYN FPM FAROPENEM
FORMUL 5 SCN 6(C N S 1-) FORMUL 11 FPM C12 H15 N O5 S FORMUL 12 SFR 4(C12 H17 N O6 S) FORMUL 16 HOH *1133(H2 O)
HELIX 1 1 VAL A 26 GLY A 41 1 16 HELIX 2 2 CYS A 69 THR A 71 5 3 HELIX 3 3 SER A 72 GLU A 85 1 14 HELIX 4 4 GLY A 89 GLN A 92 5 4 HELIX 5 5 VAL A 108 TYR A 112 5 5 HELIX 6 6 LEU A 119 TYR A 129 1 11 HELIX 7 7 ASP A 131 GLY A 143 1 13 HELIX 8 8 GLY A 144 ILE A 155 1 12 HELIX 9 9 PRO A 167 THR A 171 5 5 HELIX 10 10 SER A 182 LEU A 195 1 14 HELIX 11 11 ALA A 200 GLY A 213 1 14 HELIX 12 12 SER A 220 LEU A 225 5 6 HELIX 13 13 ARG A 275 GLU A 288 1 14 HELIX 14 14 VAL B 26 GLY B 41 1 16 HELIX 15 15 CYS B 69 THR B 71 5 3 HELIX 16 16 SER B 72 GLU B 85 1 14 HELIX 17 17 GLY B 89 GLN B 92 5 4 HELIX 18 18 LYS B 98 LEU B 102 5 5 HELIX 19 19 VAL B 108 TYR B 112 5 5 HELIX 20 20 LEU B 119 TYR B 129 1 11 HELIX 21 21 ASP B 131 GLY B 143 1 13 HELIX 22 22 GLY B 144 ILE B 155 1 12 HELIX 23 23 PRO B 167 THR B 171 5 5 HELIX 24 24 SER B 182 LEU B 195 1 14 HELIX 25 25 ALA B 200 GLY B 213 1 14 HELIX 26 26 SER B 220 LEU B 225 5 6 HELIX 27 27 ARG B 275 GLU B 288 1 14 HELIX 28 28 VAL C 26 GLY C 41 1 16 HELIX 29 29 CYS C 69 THR C 71 5 3 HELIX 30 30 SER C 72 SER C 84 1 13 HELIX 31 31 GLY C 89 GLN C 92 5 4 HELIX 32 32 VAL C 108 TYR C 112 5 5 HELIX 33 33 LEU C 119 TYR C 129 1 11 HELIX 34 34 ASP C 131 GLY C 143 1 13 HELIX 35 35 GLY C 144 ILE C 155 1 12 HELIX 36 36 PRO C 167 THR C 171 5 5 HELIX 37 37 SER C 182 LEU C 195 1 14 HELIX 38 38 ALA C 200 GLY C 213 1 14 HELIX 39 39 SER C 220 LEU C 225 5 6 HELIX 40 40 ARG C 275 GLU C 288 1 14 HELIX 41 41 VAL D 26 GLY D 41 1 16 HELIX 42 42 CYS D 69 THR D 71 5 3 HELIX 43 43 SER D 72 GLU D 85 1 14 HELIX 44 44 GLY D 89 GLN D 92 5 4 HELIX 45 45 LYS D 98 LEU D 102 5 5 HELIX 46 46 VAL D 108 VAL D 113 5 6 HELIX 47 47 LEU D 119 SER D 130 1 12 HELIX 48 48 ASP D 131 GLY D 143 1 13 HELIX 49 49 GLY D 144 ILE D 155 1 12 HELIX 50 50 PRO D 167 THR D 171 5 5 HELIX 51 51 SER D 182 LEU D 195 1 14 HELIX 52 52 ALA D 200 GLY D 213 1 14 HELIX 53 53 SER D 220 LEU D 225 5 6 HELIX 54 54 ARG D 275 GLU D 288 1 14
SHEET 1 A 5 GLN A 56 TYR A 60 0 SHEET 2 A 5 ARG A 43 ASN A 50 -1 N VAL A 46 O TYR A 60 SHEET 3 A 5 LEU A 259 THR A 266 -1 O TYR A 264 N GLY A 45 SHEET 4 A 5 THR A 243 TRP A 251 -1 N ILE A 250 O LEU A 259 SHEET 5 A 5 VAL A 230 CYS A 238 -1 N VAL A 230 O TRP A 251 SHEET 1 B 2 PHE A 66 ALA A 67 0 SHEET 2 B 2 THR A 180 THR A 181 -1 O THR A 181 N PHE A 66 SHEET 1 C 2 LYS A 94 THR A 96 0 SHEET 2 C 2 THR A 116 THR A 118 -1 O MET A 117 N MET A 95 SHEET 1 D 5 GLN B 56 TYR B 60 0 SHEET 2 D 5 ARG B 43 ASN B 50 -1 N VAL B 46 O TYR B 60 SHEET 3 D 5 LEU B 259 THR B 266 -1 O TYR B 264 N GLY B 45 SHEET 4 D 5 THR B 243 TRP B 251 -1 N ILE B 250 O LEU B 259 SHEET 5 D 5 VAL B 230 CYS B 238 -1 N GLY B 236 O ASN B 245 SHEET 1 E 2 PHE B 66 ALA B 67 0 SHEET 2 E 2 THR B 180 THR B 181 -1 O THR B 181 N PHE B 66 SHEET 1 F 2 LYS B 94 ILE B 97 0 SHEET 2 F 2 ASN B 115 THR B 118 -1 O ASN B 115 N ILE B 97 SHEET 1 G 5 GLN C 56 TYR C 60 0 SHEET 2 G 5 ARG C 43 ASN C 50 -1 N VAL C 46 O TYR C 60 SHEET 3 G 5 LEU C 259 THR C 266 -1 O TYR C 264 N GLY C 45 SHEET 4 G 5 THR C 243 TRP C 251 -1 N ILE C 250 O LEU C 259 SHEET 5 G 5 VAL C 230 CYS C 238 -1 N GLY C 236 O ASN C 245 SHEET 1 H 2 PHE C 66 ALA C 67 0 SHEET 2 H 2 THR C 180 THR C 181 -1 O THR C 181 N PHE C 66 SHEET 1 I 2 LYS C 94 ILE C 97 0 SHEET 2 I 2 ASN C 115 THR C 118 -1 O ASN C 115 N ILE C 97 SHEET 1 J 5 GLN D 56 TYR D 60 0 SHEET 2 J 5 ARG D 43 ASN D 50 -1 N VAL D 46 O TYR D 60 SHEET 3 J 5 LEU D 259 THR D 266 -1 O TYR D 264 N GLY D 45 SHEET 4 J 5 THR D 243 TRP D 251 -1 N ILE D 250 O LEU D 259 SHEET 5 J 5 VAL D 230 CYS D 238 -1 N VAL D 230 O TRP D 251 SHEET 1 K 2 PHE D 66 ALA D 67 0 SHEET 2 K 2 THR D 180 THR D 181 -1 O THR D 181 N PHE D 66 SHEET 1 L 2 LYS D 94 ILE D 97 0 SHEET 2 L 2 ASN D 115 THR D 118 -1 O ASN D 115 N ILE D 97
SSBOND 1 CYS A 69 CYS A 238 1555 1555 2.02 SSBOND 2 CYS B 69 CYS B 238 1555 1555 2.02 SSBOND 3 CYS C 69 CYS C 238 1555 1555 2.03 SSBOND 4 CYS D 69 CYS D 238 1555 1555 2.02
LINK OG SER A 70 C7 SFR A 301 1555 1555 1.30 LINK OG SER B 70 C7 SFR B 302 1555 1555 1.32 LINK OG SER C 70 C7 SFR C 303 1555 1555 1.31 LINK OG SER D 70 C7 SFR D 304 1555 1555 1.31
CISPEP 1 GLU A 166 PRO A 167 0 -1.64 CISPEP 2 GLU B 166 PRO B 167 0 -1.36 CISPEP 3 GLU C 166 PRO C 167 0 -4.37 CISPEP 4 GLU D 166 PRO D 167 0 3.37
SITE 1 AC1 5 ILE B 49 LYS B 188 ARG B 191 LYS B 192 SITE 2 AC1 5 HOH B 758 SITE 1 AC2 2 ALA A 223 LYS A 284 SITE 1 AC3 2 ARG B 61 HOH B 829 SITE 1 AC4 5 MET B 95 THR B 96 HOH B 875 HOH C 349 SITE 2 AC4 5 HOH C 547 SITE 1 AC5 3 PRO C 174 GLY C 175 HOH C 445 SITE 1 AC6 2 ARG D 256 HOH D 787 SITE 1 AC7 9 ALA B 140 HIS B 141 MET C 95 THR C 96 SITE 2 AC7 9 LYS C 137 ALA C 140 HIS C 141 HOH C 339 SITE 3 AC7 9 HOH C 390 SITE 1 AC8 15 CYS A 69 SER A 70 LYS A 73 TRP A 105 SITE 2 AC8 15 SER A 130 ASN A 132 GLU A 166 ASN A 170 SITE 3 AC8 15 LYS A 234 THR A 235 GLY A 236 ALA A 237 SITE 4 AC8 15 HOH A 361 HOH A 451 HOH A 598 SITE 1 AC9 13 CYS B 69 SER B 70 TRP B 105 SER B 130 SITE 2 AC9 13 ASN B 132 GLU B 166 ASN B 170 THR B 235 SITE 3 AC9 13 GLY B 236 ALA B 237 HOH B 612 HOH B 629 SITE 4 AC9 13 HOH B 697 SITE 1 BC1 14 HOH A 590 CYS C 69 SER C 70 LYS C 73 SITE 2 BC1 14 TRP C 105 SER C 130 ASN C 132 GLU C 166 SITE 3 BC1 14 ASN C 170 THR C 235 GLY C 236 ALA C 237 SITE 4 BC1 14 HOH C 389 HOH C 564 SITE 1 BC2 14 CYS D 69 SER D 70 LYS D 73 TRP D 105 SITE 2 BC2 14 SER D 130 ASN D 132 GLU D 166 ASN D 170 SITE 3 BC2 14 THR D 216 THR D 235 GLY D 236 ALA D 237 SITE 4 BC2 14 HOH D 670 HOH D 671
CRYST1 187.116 73.244 103.504 90.00 121.69 90.00 C 1 2 1 16
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 0.005344 0.000000 0.003299 0.00000
SCALE2 0.000000 0.013653 -0.000001 0.00000
SCALE3 0.000000 0.000000 0.011354 0.00000