10 20 30 40 50 60 70 80 3BFG - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 21-NOV-07 3BFG
TITLE CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH MEROPENEM
CAVEAT 3BFG CHIRALITY ERRORS AT C17 CHIRAL ATOMS OF LIGANDS MER A301, CAVEAT 2 3BFG B302, C303 AND D304.
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, MEROPENEM, ACYL-ENZYME
EXPDTA X-RAY DIFFRACTION
AUTHOR L.PERNOT,S.PETRELLA,W.SOUGAKOFF
REVDAT 3 16-MAY-12 3BFG 1 CAVEAT VERSN REVDAT 2 24-FEB-09 3BFG 1 VERSN REVDAT 1 18-DEC-07 3BFG 0
JRNL AUTH L.PERNOT,S.PETRELLA,W.SOUGAKOFF JRNL TITL ACYL-INTERMEDIATE STRUCTURES OF THE CLASS A BETA-LACTAMASE JRNL TITL 2 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 STUDY OF REMARK 1 TITL 2 THE CLASS A BETA-LACTAMASE SED-1 AND ITS MUTANT SED-G238C REMARK 1 TITL 3 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.10 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) (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 72269 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) : 0.198 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3076 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9645 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 383 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 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 : 104 REMARK 3 SOLVENT ATOMS : 823 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.56000 REMARK 3 B22 (A**2) : -4.56000 REMARK 3 B33 (A**2) : 11.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.29 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.94 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 3BFG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-NOV-07. REMARK 100 THE RCSB ID CODE IS RCSB045453.
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 : 75348 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 34.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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 (%): 54.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 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 94.07100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.58850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 94.07100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.58850 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: 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 OG SER A 70 O6 MER A 301 2.11 REMARK 500 OG SER B 70 O6 MER B 302 2.18 REMARK 500 OG SER C 70 O6 MER C 303 2.19 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 CYS D 69 CA - CB - SG ANGL. DEV. = 10.3 DEGREES REMARK 500 CYS D 238 CA - CB - SG ANGL. DEV. = 9.3 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 -139.91 53.67 REMARK 500 THR A 103 -150.40 -115.98 REMARK 500 ASN A 115 -166.64 -118.90 REMARK 500 SER A 220 -130.89 -100.32 REMARK 500 ASP A 246 134.14 -170.49 REMARK 500 GLU A 254 -126.66 50.46 REMARK 500 ASN B 54 16.36 59.88 REMARK 500 CYS B 69 -139.47 55.92 REMARK 500 THR B 103 -145.16 -122.46 REMARK 500 SER B 220 -130.83 -103.20 REMARK 500 ASP B 246 136.97 -172.99 REMARK 500 GLU B 254 -122.10 52.37 REMARK 500 CYS C 69 -138.09 53.10 REMARK 500 THR C 103 -150.04 -117.38 REMARK 500 SER C 220 -127.98 -98.51 REMARK 500 ASP C 240 161.37 -47.11 REMARK 500 ASP C 246 134.23 -172.23 REMARK 500 GLU C 254 -126.57 51.08 REMARK 500 ASP D 53 10.75 -144.42 REMARK 500 CYS D 69 -140.62 53.14 REMARK 500 THR D 103 -141.45 -115.91 REMARK 500 ASN D 115 -161.10 -126.18 REMARK 500 SER D 220 -122.81 -107.20 REMARK 500 ASP D 246 132.43 -173.28 REMARK 500 GLU D 254 -129.74 51.49 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 A 376 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 451 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH C 539 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH D 400 DISTANCE = 5.34 ANGSTROMS REMARK 525 HOH D 451 DISTANCE = 5.16 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MER A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MER B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MER C 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MER 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: 3BFF RELATED DB: PDB REMARK 900 CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH FAROPENEM
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 3BFG A 26 290 UNP Q93PQ0 Q93PQ0_9ENTR 34 295 DBREF 3BFG B 26 290 UNP Q93PQ0 Q93PQ0_9ENTR 34 295 DBREF 3BFG C 26 290 UNP Q93PQ0 Q93PQ0_9ENTR 34 295 DBREF 3BFG D 26 290 UNP Q93PQ0 Q93PQ0_9ENTR 34 295
SEQADV 3BFG CYS A 238 UNP Q93PQ0 GLY 245 ENGINEERED SEQADV 3BFG CYS B 238 UNP Q93PQ0 GLY 245 ENGINEERED SEQADV 3BFG CYS C 238 UNP Q93PQ0 GLY 245 ENGINEERED SEQADV 3BFG 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 MER A 301 26 HET MER B 302 26 HET MER C 303 26 HET MER D 304 26
HETNAM MER (4R,5S)-3-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3- HETNAM 2 MER YL]SULFANYL}-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4- HETNAM 3 MER METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
HETSYN MER MEROPENEM, BOUND FORM
FORMUL 5 MER 4(C17 H27 N3 O5 S) FORMUL 9 HOH *823(H2 O)
HELIX 1 1 GLN A 27 GLY A 41 1 15 HELIX 2 2 CYS A 69 THR A 71 5 3 HELIX 3 3 SER A 72 HIS A 87 1 16 HELIX 4 4 GLY A 89 GLN A 92 5 4 HELIX 5 5 VAL A 108 VAL A 113 5 6 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 GLN B 27 GLY B 41 1 15 HELIX 15 15 THR B 71 SER B 84 1 14 HELIX 16 16 GLY B 89 GLN B 92 5 4 HELIX 17 17 LYS B 98 LEU B 102 5 5 HELIX 18 18 VAL B 108 TYR B 112 5 5 HELIX 19 19 LEU B 119 TYR B 129 1 11 HELIX 20 20 ASP B 131 GLY B 143 1 13 HELIX 21 21 GLY B 144 ILE B 155 1 12 HELIX 22 22 PRO B 167 THR B 171 5 5 HELIX 23 23 SER B 182 LEU B 195 1 14 HELIX 24 24 ALA B 200 GLY B 213 1 14 HELIX 25 25 SER B 220 LEU B 225 5 6 HELIX 26 26 ARG B 275 THR B 287 1 13 HELIX 27 27 GLN C 27 GLY C 41 1 15 HELIX 28 28 CYS C 69 THR C 71 5 3 HELIX 29 29 SER C 72 SER C 84 1 13 HELIX 30 30 GLY C 89 GLN C 92 5 4 HELIX 31 31 VAL C 108 TYR C 112 5 5 HELIX 32 32 LEU C 119 TYR C 129 1 11 HELIX 33 33 ASP C 131 GLY C 143 1 13 HELIX 34 34 GLY C 144 ILE C 155 1 12 HELIX 35 35 PRO C 167 THR C 171 5 5 HELIX 36 36 SER C 182 LEU C 195 1 14 HELIX 37 37 ALA C 200 GLY C 213 1 14 HELIX 38 38 SER C 220 LEU C 225 5 6 HELIX 39 39 ARG C 275 GLU C 288 1 14 HELIX 40 40 VAL D 26 GLY D 41 1 16 HELIX 41 41 CYS D 69 THR D 71 5 3 HELIX 42 42 SER D 72 GLU D 85 1 14 HELIX 43 43 GLY D 89 GLN D 92 5 4 HELIX 44 44 LYS D 98 LEU D 102 5 5 HELIX 45 45 VAL D 108 VAL D 113 5 6 HELIX 46 46 LEU D 119 TYR D 129 1 11 HELIX 47 47 ASP D 131 GLY D 143 1 13 HELIX 48 48 GLY D 144 ILE D 155 1 12 HELIX 49 49 PRO D 167 THR D 171 5 5 HELIX 50 50 SER D 182 LEU D 195 1 14 HELIX 51 51 ALA D 200 GLY D 213 1 14 HELIX 52 52 SER D 220 LEU D 225 5 6 HELIX 53 53 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 GLY A 236 O ASN A 245 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 THR C 266 N ARG C 43 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 GLY D 236 O ASN D 245 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 THR D 96 0 SHEET 2 L 2 THR D 116 THR D 118 -1 O MET D 117 N MET D 95
SSBOND 1 CYS A 69 CYS A 238 1555 1555 2.04 SSBOND 2 CYS B 69 CYS B 238 1555 1555 2.03 SSBOND 3 CYS C 69 CYS C 238 1555 1555 2.04 SSBOND 4 CYS D 69 CYS D 238 1555 1555 2.03
LINK OG SER A 70 C1 MER A 301 1555 1555 1.31 LINK OG SER B 70 C1 MER B 302 1555 1555 1.32 LINK OG SER C 70 C1 MER C 303 1555 1555 1.32 LINK OG SER D 70 C1 MER D 304 1555 1555 1.32
CISPEP 1 GLU A 166 PRO A 167 0 1.83 CISPEP 2 GLU B 166 PRO B 167 0 0.10 CISPEP 3 GLU C 166 PRO C 167 0 0.06 CISPEP 4 GLU D 166 PRO D 167 0 0.62
SITE 1 AC1 16 CYS A 69 SER A 70 SER A 130 ASN A 132 SITE 2 AC1 16 GLU A 166 ASN A 170 THR A 216 LYS A 234 SITE 3 AC1 16 THR A 235 GLY A 236 ALA A 237 TRP A 274 SITE 4 AC1 16 LYS A 276 HOH A 354 HOH A 412 HOH A 427 SITE 1 AC2 13 CYS B 69 SER B 70 LYS B 73 TRP B 105 SITE 2 AC2 13 SER B 130 ASN B 132 THR B 216 LYS B 234 SITE 3 AC2 13 THR B 235 GLY B 236 ALA B 237 HOH B 376 SITE 4 AC2 13 HOH B 439 SITE 1 AC3 15 CYS C 69 SER C 70 LYS C 73 TRP C 105 SITE 2 AC3 15 SER C 130 ASN C 132 GLU C 166 THR C 216 SITE 3 AC3 15 LYS C 234 THR C 235 GLY C 236 ALA C 237 SITE 4 AC3 15 HOH C 471 HOH C 499 THR D 86 SITE 1 AC4 13 CYS D 69 SER D 70 LYS D 73 TRP D 105 SITE 2 AC4 13 SER D 130 ASN D 132 THR D 216 LYS D 234 SITE 3 AC4 13 THR D 235 GLY D 236 ALA D 237 HOH D 352 SITE 4 AC4 13 HOH D 425
CRYST1 188.142 73.177 105.384 90.00 122.42 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 0.005315 0.000000 0.003376 0.00000
SCALE2 0.000000 0.013665 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011241 0.00000