10 20 30 40 50 60 70 80 2C5W - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/HYDROLASE 02-NOV-05 2C5W
TITLE PENICILLIN-BINDING PROTEIN 1A (PBP-1A) ACYL-ENZYME COMPLEX TITLE 2 (CEFOTAXIME) FROM STREPTOCOCCUS PNEUMONIAE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GLYLOSYLTRANSFERASE DOMAIN, RESIDUES 51-66; COMPND 5 SYNONYM: PBP-1A, EXPORTED PROTEIN 2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PENICILLIN-BINDING PROTEIN 1A; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: TRANSPEPTIDASE DOMAIN, RESIDUES 267-650; COMPND 11 SYNONYM: PBP-1A, EXPORTED PROTEIN 2; COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 171101; SOURCE 4 STRAIN: R6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: MC1061; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJAH143; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 12 ORGANISM_TAXID: 171101; SOURCE 13 STRAIN: R6; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: MC1061; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PJAH143
KEYWDS PEPTIDOGLYCAN SYNTHESIS, TRANSFERASE-HYDROLASE COMPLEX, KEYWDS 2 ANTIBIOTIC RESISTANCE, CELL SHAPE, MULTIFUNCTIONAL ENZYME
EXPDTA X-RAY DIFFRACTION
AUTHOR C.CONTRERAS-MARTEL,V.JOB,A.-M.DI GUILMI,T.VERNET,O.DIDEBERG, AUTHOR 2 A.DESSEN
REVDAT 4 03-AUG-11 2C5W 1 HEADER KEYWDS REMARK SEQADV REVDAT 4 2 HETNAM HETSYN VERSN REVDAT 3 24-FEB-09 2C5W 1 VERSN REVDAT 2 04-JAN-06 2C5W 1 JRNL REVDAT 1 07-DEC-05 2C5W 0
JRNL AUTH C.CONTRERAS-MARTEL,V.JOB,A.-M.DI GUILMI,T.VERNET, JRNL AUTH 2 O.DIDEBERG,A.DESSEN JRNL TITL CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 1A JRNL TITL 2 (PBP1A) REVEALS A MUTATIONAL HOTSPOT IMPLICATED IN JRNL TITL 3 BETA-LACTAM RESISTANCE IN STREPTOCOCCUS JRNL TITL 4 PNEUMONIAE. JRNL REF J.MOL.BIOL. V. 355 684 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16316661 JRNL DOI 10.1016/J.JMB.2005.10.030
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.JOB,A.-M.DI GUILMI,L.MARTIN,T.VERNET,O.DIDEBERG, REMARK 1 AUTH 2 A.DESSEN REMARK 1 TITL STRUCTURAL STUDIES OF THE TRANSPEPTIDASE DOMAIN OF REMARK 1 TITL 2 PBP1A FROM STREPTOCOCCUS PNEUMONIAE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 1067 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12777776 REMARK 1 DOI 10.1107/S0907444903006954 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.-M.DI GUILMI,N.MOUZ,J.-P.ANDRIEU,J.HOSKINS, REMARK 1 AUTH 2 S.R.JASKUNAS,J.GAGNON,O.DIDEBERG,T.VERNET REMARK 1 TITL IDENTIFICATION, PURIFICATION, AND REMARK 1 TITL 2 CHARACTHERIZATION OF TRANSPEPTIDASE AND REMARK 1 TITL 3 GLYCOSYLTRANSFERASE DOMAINS OF STREPTOCOCCUS REMARK 1 TITL 4 PNEUMONIAE PENICILLIN-BINDING PROTEIN 1A REMARK 1 REF J.BACTERIOL. V. 180 5652 1998 REMARK 1 REFN ISSN 0021-9193 REMARK 1 PMID 9791115
REMARK 2 REMARK 2 RESOLUTION. 2.55 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4488958.94 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 17350 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) : 0.234 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.8 REMARK 3 FREE R VALUE TEST SET COUNT : 839 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.5 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1757 REMARK 3 BIN R VALUE (WORKING SET) : 0.344 REMARK 3 BIN FREE R VALUE : 0.388 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.8 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 89 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.041 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3170 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.16 REMARK 3 B22 (A**2) : -18.94 REMARK 3 B33 (A**2) : 15.78 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.53 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) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.71 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.4 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.1 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.75 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) : 2.18 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.52 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.25 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.62 ; 2.50 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.342401 REMARK 3 BSOL : 39.754 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CEF.PAR REMARK 3 PARAMETER FILE 3 : EGL_XPLOR.PAR REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : WATER.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CEF.TOP REMARK 3 TOPOLOGY FILE 3 : EGL_XPLOR.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : WATER.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2C5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-05. REMARK 100 THE PDBE ID CODE IS EBI-26243.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16766 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: PHASER, SHARP REMARK 200 STARTING MODEL: PDB ENTRY 2BG4 REMARK 200 REMARK 200 REMARK: PARTIAL PHASING INFORMATION FROM DIFFERENT SOURCES WAS REMARK 200 DEVISED USING SHARP
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG1000,50 MM NACL, 5MM REMARK 280 ZNSO4,50MM TRIS PH 7.0
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 27.42500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.42500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 56.18800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 91.68650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 56.18800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 91.68650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.42500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 56.18800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 91.68650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.42500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 56.18800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 91.68650 REMARK 290 SMTRY3 8 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 300 REMARK 300 DETAILS:PBP-1A IS A MONOMER IN SOLUTION, BUT REMARK 300 SINCE IN THIS ENTRYTHERE IS A CLEAVED PEPTIDE REMARK 300 FROM THE SAME PROTEIN (CHAIN A)ASSOCIATED WITH REMARK 300 THE TRANSPEPTIDASE DOMAIN OFPBP-1A (CHAIN B), THE REMARK 300 ENTRY IS MARKED AS 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -126.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 B 370 - O1 PCZ B 1370 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 VAL B 354 N - CA - C ANGL. DEV. = -17.8 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 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 ASP A 57 -159.40 -88.51 REMARK 500 ASN B 267 -53.70 -142.09 REMARK 500 LEU B 291 1.67 -57.42 REMARK 500 ASP B 324 -176.62 -175.07 REMARK 500 SER B 351 55.94 -112.35 REMARK 500 SER B 352 58.51 -96.64 REMARK 500 ASN B 353 106.93 -38.60 REMARK 500 THR B 392 136.87 -39.46 REMARK 500 ASP B 396 77.12 -101.19 REMARK 500 ILE B 465 13.98 -143.52 REMARK 500 LYS B 504 139.91 -173.17 REMARK 500 THR B 588 -163.09 -109.21 REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 309 ND1 REMARK 620 2 GLU B 514 OE1 82.0 REMARK 620 3 GLU B 514 OE2 89.2 55.5 REMARK 620 4 HOH B2040 O 91.6 114.9 59.8 REMARK 620 5 HOH B2063 O 110.3 80.8 129.5 155.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 395 ND1 REMARK 620 2 GLU B 397 OE1 94.1 REMARK 620 3 GLU B 397 OE2 89.7 51.9 REMARK 620 4 GLU B 435 OE1 106.0 122.1 164.0 REMARK 620 5 GLU B 435 OE2 141.3 77.8 112.5 52.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2064 O REMARK 620 2 HIS B 460 ND1 107.8 REMARK 620 3 HIS B 571 NE2 107.1 101.0 REMARK 620 4 GLU B 566 OE1 136.6 100.0 99.3 REMARK 620 5 GLU B 566 OE2 85.7 126.2 125.0 50.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 704 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 503 NE2 REMARK 620 2 GLU B 318 OE2 152.0 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 711 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 712 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PCZ B1370
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C6W RELATED DB: PDB REMARK 900 PENICILLIN-BINDING PROTEIN 1A (PBP-1A) FROM REMARK 900 STREPTOCOCCUS PNEUMONIAE
REMARK 999 REMARK 999 SEQUENCE REMARK 999 EXTRA PEPTIDE FROM THE GLYLOSYLTRANSFERASE DOMAIN, REMARK 999 RESIDUES 51-66. THE SEQUENCE IN THE SEQRES RECORDS REMARK 999 BELOW IS THE OBSERVED SEQUENCE AND THAT REPORTED REMARK 999 BY A.-M.DI GUILMI ET AL.
DBREF 2C5W A 51 66 UNP Q8DR59 PBPA_STRR6 51 66 DBREF 2C5W B 266 650 UNP Q8DR59 PBPA_STRR6 266 650
SEQADV 2C5W THR B 540 UNP Q8DR59 SER 540 CONFLICT
SEQRES 1 A 16 THR SER SER LYS ILE TYR ASP ASN LYS ASN GLN LEU ILE SEQRES 2 A 16 ALA ASP LEU SEQRES 1 B 385 SER ASN TYR PRO ALA TYR MET ASP ASN TYR LEU LYS GLU SEQRES 2 B 385 VAL ILE ASN GLN VAL GLU GLU GLU THR GLY TYR ASN LEU SEQRES 3 B 385 LEU THR THR GLY MET ASP VAL TYR THR ASN VAL ASP GLN SEQRES 4 B 385 GLU ALA GLN LYS HIS LEU TRP ASP ILE TYR ASN THR ASP SEQRES 5 B 385 GLU TYR VAL ALA TYR PRO ASP ASP GLU LEU GLN VAL ALA SEQRES 6 B 385 SER THR ILE VAL ASP VAL SER ASN GLY LYS VAL ILE ALA SEQRES 7 B 385 GLN LEU GLY ALA ARG HIS GLN SER SER ASN VAL SER PHE SEQRES 8 B 385 GLY ILE ASN GLN ALA VAL GLU THR ASN ARG ASP TRP GLY SEQRES 9 B 385 SER THR MET LYS PRO ILE THR ASP TYR ALA PRO ALA LEU SEQRES 10 B 385 GLU TYR GLY VAL TYR GLU SER THR ALA THR ILE VAL HIS SEQRES 11 B 385 ASP GLU PRO TYR ASN TYR PRO GLY THR ASN THR PRO VAL SEQRES 12 B 385 TYR ASN TRP ASP ARG GLY TYR PHE GLY ASN ILE THR LEU SEQRES 13 B 385 GLN TYR ALA LEU GLN GLN SER ARG ASN VAL PRO ALA VAL SEQRES 14 B 385 GLU THR LEU ASN LYS VAL GLY LEU ASN ARG ALA LYS THR SEQRES 15 B 385 PHE LEU ASN GLY LEU GLY ILE ASP TYR PRO SER ILE HIS SEQRES 16 B 385 TYR SER ASN ALA ILE SER SER ASN THR THR GLU SER ASP SEQRES 17 B 385 LYS LYS TYR GLY ALA SER SER GLU LYS MET ALA ALA ALA SEQRES 18 B 385 TYR ALA ALA PHE ALA ASN GLY GLY THR TYR TYR LYS PRO SEQRES 19 B 385 MET TYR ILE HIS LYS VAL VAL PHE SER ASP GLY SER GLU SEQRES 20 B 385 LYS GLU PHE SER ASN VAL GLY THR ARG ALA MET LYS GLU SEQRES 21 B 385 THR THR ALA TYR MET MET THR ASP MET MET LYS THR VAL SEQRES 22 B 385 LEU THR TYR GLY THR GLY ARG ASN ALA TYR LEU ALA TRP SEQRES 23 B 385 LEU PRO GLN ALA GLY LYS THR GLY THR SER ASN TYR THR SEQRES 24 B 385 ASP GLU GLU ILE GLU ASN HIS ILE LYS THR SER GLN PHE SEQRES 25 B 385 VAL ALA PRO ASP GLU LEU PHE ALA GLY TYR THR ARG LYS SEQRES 26 B 385 TYR SER MET ALA VAL TRP THR GLY TYR SER ASN ARG LEU SEQRES 27 B 385 THR PRO LEU VAL GLY ASN GLY LEU THR VAL ALA ALA LYS SEQRES 28 B 385 VAL TYR ARG SER MET MET THR TYR LEU SER GLU GLY SER SEQRES 29 B 385 ASN PRO GLU ASP TRP ASN ILE PRO GLU GLY LEU TYR ARG SEQRES 30 B 385 ASN GLY GLU PHE VAL PHE LYS ASN
HET ZN B 701 1 HET ZN B 702 1 HET ZN B 703 1 HET ZN B 704 1 HET ZN B 705 1 HET CL B 706 1 HET CL B 707 1 HET EDO B 711 4 HET EDO B 712 4 HET PCZ B1370 26
HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PCZ (2R)-2-[(1R)-1-{[(2Z)-2-(2-AMINO-1,3-THIAZOL- HETNAM 2 PCZ 4-YL)-2-(METHOXYIMINO)ACETYL]AMINO}-2- HETNAM 3 PCZ OXOETHYL]-5-METHYLIDENE-5,6-DIHYDRO-2H-1,3-THIAZINE- HETNAM 4 PCZ 4-CARBOXYLIC ACID
HETSYN EDO ETHYLENE GLYCOL HETSYN PCZ CEFOTAXIME PRODUCT, OPEN FORM
FORMUL 3 ZN 5(ZN 2+) FORMUL 8 CL 2(CL 1-) FORMUL 10 EDO 2(C2 H6 O2) FORMUL 12 PCZ C14 H15 N5 O6 S2 FORMUL 13 HOH *65(H2 O1)
HELIX 1 1 PRO B 269 TYR B 271 5 3 HELIX 2 2 MET B 272 GLY B 288 1 17 HELIX 3 3 ASP B 303 THR B 316 1 14 HELIX 4 4 TRP B 368 SER B 370 5 3 HELIX 5 5 THR B 371 ASP B 377 1 7 HELIX 6 6 ASP B 377 TYR B 384 1 8 HELIX 7 7 LEU B 421 GLN B 427 1 7 HELIX 8 8 ARG B 429 GLY B 441 1 13 HELIX 9 9 GLY B 441 GLY B 451 1 11 HELIX 10 10 HIS B 460 ILE B 465 5 6 HELIX 11 11 SER B 479 ASN B 492 1 14 HELIX 12 12 LYS B 524 GLY B 542 1 19 HELIX 13 13 GLY B 544 TYR B 548 5 5 HELIX 14 14 THR B 564 HIS B 571 1 8 HELIX 15 15 ASN B 609 LEU B 611 5 3 HELIX 16 16 THR B 612 GLU B 627 1 16
SHEET 1 AA 5 LEU A 62 ASP A 65 0 SHEET 2 AA 5 LYS A 54 TYR A 56 -1 O ILE A 55 N ILE A 63 SHEET 3 AA 5 MET B 296 THR B 300 1 O MET B 296 N LYS A 54 SHEET 4 AA 5 ILE B 502 PHE B 507 -1 N HIS B 503 O TYR B 299 SHEET 5 AA 5 GLU B 512 GLU B 514 -1 O LYS B 513 N VAL B 505 SHEET 1 BA 5 VAL B 341 LEU B 345 0 SHEET 2 BA 5 GLN B 328 ASP B 335 -1 O SER B 331 N LEU B 345 SHEET 3 BA 5 TYR B 591 GLY B 598 -1 O SER B 592 N VAL B 334 SHEET 4 BA 5 GLU B 582 TYR B 587 -1 O GLU B 582 N THR B 597 SHEET 5 BA 5 ALA B 555 THR B 560 -1 O ALA B 555 N TYR B 587 SHEET 1 BB 2 ILE B 393 ASP B 396 0 SHEET 2 BB 2 GLY B 417 THR B 420 -1 O GLY B 417 N ASP B 396 SHEET 1 BC 2 THR B 495 TYR B 497 0 SHEET 2 BC 2 GLY B 519 ARG B 521 -1 O THR B 520 N TYR B 496 SHEET 1 BD 2 VAL B 578 ALA B 579 0 SHEET 2 BD 2 LEU B 606 VAL B 607 -1 O LEU B 606 N ALA B 579 SHEET 1 BE 2 LEU B 640 ASN B 643 0 SHEET 2 BE 2 PHE B 646 LYS B 649 -1 O PHE B 646 N ASN B 643
LINK OG SER B 370 C1 PCZ B1370 1555 1555 1.36 LINK ZN ZN B 701 OE1 GLU B 514 1555 6555 2.26 LINK ZN ZN B 701 OE2 GLU B 514 1555 6555 2.43 LINK ZN ZN B 701 O HOH B2040 1555 6555 2.42 LINK ZN ZN B 701 O HOH B2063 1555 1555 2.70 LINK ZN ZN B 701 ND1 HIS B 309 1555 1555 2.40 LINK ZN ZN B 702 OE1 GLU B 397 1555 4555 2.58 LINK ZN ZN B 702 OE2 GLU B 397 1555 4555 2.41 LINK ZN ZN B 702 OE1 GLU B 435 1555 1555 2.38 LINK ZN ZN B 702 OE2 GLU B 435 1555 1555 2.55 LINK ZN ZN B 702 ND1 HIS B 395 1555 1555 2.10 LINK ZN ZN B 703 NE2 HIS B 571 1555 3655 2.15 LINK ZN ZN B 703 OE1 GLU B 566 1555 3655 2.66 LINK ZN ZN B 703 OE2 GLU B 566 1555 3655 2.43 LINK ZN ZN B 703 ND1 HIS B 460 1555 1555 2.28 LINK ZN ZN B 703 O HOH B2064 1555 1555 2.29 LINK ZN ZN B 704 OE2 GLU B 318 1555 6554 2.74 LINK ZN ZN B 704 NE2 HIS B 503 1555 1555 2.41 LINK ZN ZN B 705 ND1 HIS B 349 1555 1555 2.54
SITE 1 AC1 4 HIS B 309 GLU B 514 HOH B2040 HOH B2063 SITE 1 AC2 3 HIS B 395 GLU B 397 GLU B 435 SITE 1 AC3 4 HIS B 460 GLU B 566 HIS B 571 HOH B2064 SITE 1 AC4 2 GLU B 318 HIS B 503 SITE 1 AC5 1 HIS B 349 SITE 1 AC6 2 ILE B 393 ASN B 418 SITE 1 AC7 2 ASP B 297 GLU B 638 SITE 1 AC8 3 SER B 462 ASN B 562 EDO B 712 SITE 1 AC9 5 TYR B 409 ASN B 410 TRP B 411 EDO B 711 SITE 2 AC9 5 PCZ B1370 SITE 1 BC1 12 ASP B 367 SER B 370 TRP B 411 SER B 428 SITE 2 BC1 12 ASN B 430 ILE B 465 THR B 558 GLY B 559 SITE 3 BC1 12 THR B 560 SER B 561 ASN B 562 EDO B 712
CRYST1 112.376 183.373 54.850 90.00 90.00 90.00 C 2 2 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 0.008899 0.000000 0.000000 0.00000
SCALE2 0.000000 0.005453 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018232 0.00000