HEADER PENICILLIN-BINDING PROTEIN/ANTIBIOTIC 18-NOV-11 3UPP TITLE STRUCTURE OF PENICILLIN-BINDING PROTEIN A FROM M. TUBERCULOSIS: TITLE 2 CEFTRIXAONE ACYL-ENZYME COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 35-491; COMPND 5 SYNONYM: PBPA; COMPND 6 EC: 3.4.16.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: MT0019, MTCY10H4.16C, PBPA, RV0016C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7HTB KEYWDS TRANSPEPTIDASE, PEPTIDOGLYCAN, BETA-LACTAM, PENICILLIN-BINDING KEYWDS 2 PROTEIN-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.DAVIES,A.FEDOROVICH REVDAT 4 16-OCT-24 3UPP 1 REMARK REVDAT 3 13-SEP-23 3UPP 1 SEQADV LINK REVDAT 2 19-SEP-18 3UPP 1 COMPND SOURCE REMARK HET REVDAT 2 2 1 HETNAM HETSYN FORMUL LINK REVDAT 2 3 1 ATOM REVDAT 1 24-OCT-12 3UPP 0 JRNL AUTH A.FEDAROVICH,R.A.NICHOLAS,C.DAVIES JRNL TITL THE ROLE OF THE BETA5-ALPHA11 LOOP IN THE ACTIVE-SITE JRNL TITL 2 DYNAMICS OF ACYLATED PENICILLIN-BINDING PROTEIN A FROM JRNL TITL 3 MYCOBACTERIUM TUBERCULOSIS JRNL REF J.MOL.BIOL. V. 418 316 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22365933 JRNL DOI 10.1016/J.JMB.2012.02.021 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 32018 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1708 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2144 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6517 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -0.67000 REMARK 3 B12 (A**2) : 0.22000 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): 0.531 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.275 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.223 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.760 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6716 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9181 ; 1.360 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 882 ; 6.550 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 263 ;35.338 ;23.422 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 991 ;17.210 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;17.285 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1046 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5204 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3184 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4669 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.132 ; 0.200 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): 85 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.183 ; 0.200 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): 4500 ; 0.573 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7076 ; 0.999 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2451 ; 1.448 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2105 ; 2.413 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3UPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-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 : APS REMARK 200 BEAMLINE : 22-ID 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 : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33749 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 45.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.62300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 3LO7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2 M NACL, 0.1 M BIS REMARK 280 -TRIS PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.76133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.52267 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 50.64200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 84.40333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.88067 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 GLY A 30 REMARK 465 ALA A 31 REMARK 465 MET A 32 REMARK 465 GLY A 33 REMARK 465 SER A 34 REMARK 465 ARG A 35 REMARK 465 ALA A 36 REMARK 465 ASP A 37 REMARK 465 PRO A 38 REMARK 465 ARG A 39 REMARK 465 ASN A 40 REMARK 465 GLN A 41 REMARK 465 ARG A 42 REMARK 465 VAL A 43 REMARK 465 GLY A 489 REMARK 465 GLU A 490 REMARK 465 PRO A 491 REMARK 465 GLY B 30 REMARK 465 ALA B 31 REMARK 465 MET B 32 REMARK 465 GLY B 33 REMARK 465 SER B 34 REMARK 465 ARG B 35 REMARK 465 ALA B 36 REMARK 465 ASP B 37 REMARK 465 PRO B 38 REMARK 465 ARG B 39 REMARK 465 ASN B 40 REMARK 465 GLN B 41 REMARK 465 ARG B 42 REMARK 465 VAL B 43 REMARK 465 LEU B 44 REMARK 465 LEU B 45 REMARK 465 ASP B 46 REMARK 465 GLU B 47 REMARK 465 TYR B 48 REMARK 465 SER B 49 REMARK 465 GLY B 489 REMARK 465 GLU B 490 REMARK 465 PRO B 491 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 SER A 96 -143.40 68.28 REMARK 500 ALA A 99 -130.90 49.38 REMARK 500 SER A 180 -164.00 -114.97 REMARK 500 GLU A 241 134.42 -38.26 REMARK 500 GLN A 339 -139.99 -118.85 REMARK 500 LYS A 340 -122.51 45.08 REMARK 500 ILE A 379 -31.84 -133.35 REMARK 500 ALA A 447 146.95 -170.93 REMARK 500 SER B 96 -142.85 68.38 REMARK 500 ALA B 99 -135.29 49.10 REMARK 500 ASP B 128 70.04 67.51 REMARK 500 SER B 180 -165.28 -115.29 REMARK 500 GLN B 339 -143.55 -122.60 REMARK 500 LYS B 340 -113.27 54.84 REMARK 500 ALA B 415 93.68 -60.71 REMARK 500 PRO B 417 -72.47 -18.39 REMARK 500 ALA B 451 71.98 -155.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG B 127 ASP B 128 54.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE STARTING ANTIBIOTIC IS CEFTRIAXONE. UPON ACYLATION THIS REMARK 600 COMPOUND BECOMES COVALENTLY BOUND TO THE PBP REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PCZ A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PCZ B 800 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LO7 RELATED DB: PDB REMARK 900 NATIVE STRUCTURE WITH TAG REMARK 900 RELATED ID: 3UN7 RELATED DB: PDB REMARK 900 NATIVE STRUCTURE REMARK 900 RELATED ID: 3UPN RELATED DB: PDB REMARK 900 RELATED ID: 3UPO RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE MUTATION G384R OCCURED DURING PCR DBREF 3UPP A 35 491 UNP P71586 PBPA_MYCTU 35 491 DBREF 3UPP B 35 491 UNP P71586 PBPA_MYCTU 35 491 SEQADV 3UPP GLY A 30 UNP P71586 EXPRESSION TAG SEQADV 3UPP ALA A 31 UNP P71586 EXPRESSION TAG SEQADV 3UPP MET A 32 UNP P71586 EXPRESSION TAG SEQADV 3UPP GLY A 33 UNP P71586 EXPRESSION TAG SEQADV 3UPP SER A 34 UNP P71586 EXPRESSION TAG SEQADV 3UPP ARG A 384 UNP P71586 GLY 384 SEE REMARK 999 SEQADV 3UPP GLY B 30 UNP P71586 EXPRESSION TAG SEQADV 3UPP ALA B 31 UNP P71586 EXPRESSION TAG SEQADV 3UPP MET B 32 UNP P71586 EXPRESSION TAG SEQADV 3UPP GLY B 33 UNP P71586 EXPRESSION TAG SEQADV 3UPP SER B 34 UNP P71586 EXPRESSION TAG SEQADV 3UPP ARG B 384 UNP P71586 GLY 384 SEE REMARK 999 SEQRES 1 A 462 GLY ALA MET GLY SER ARG ALA ASP PRO ARG ASN GLN ARG SEQRES 2 A 462 VAL LEU LEU ASP GLU TYR SER ARG GLN ARG GLY GLN ILE SEQRES 3 A 462 THR ALA GLY GLY GLN LEU LEU ALA TYR SER VAL ALA THR SEQRES 4 A 462 ASP GLY ARG PHE ARG PHE LEU ARG VAL TYR PRO ASN PRO SEQRES 5 A 462 GLU VAL TYR ALA PRO VAL THR GLY PHE TYR SER LEU ARG SEQRES 6 A 462 TYR SER SER THR ALA LEU GLU ARG ALA GLU ASP PRO ILE SEQRES 7 A 462 LEU ASN GLY SER ASP ARG ARG LEU PHE GLY ARG ARG LEU SEQRES 8 A 462 ALA ASP PHE PHE THR GLY ARG ASP PRO ARG GLY GLY ASN SEQRES 9 A 462 VAL ASP THR THR ILE ASN PRO ARG ILE GLN GLN ALA GLY SEQRES 10 A 462 TRP ASP ALA MET GLN GLN GLY CYS TYR GLY PRO CYS LYS SEQRES 11 A 462 GLY ALA VAL VAL ALA LEU GLU PRO SER THR GLY LYS ILE SEQRES 12 A 462 LEU ALA LEU VAL SER SER PRO SER TYR ASP PRO ASN LEU SEQRES 13 A 462 LEU ALA SER HIS ASN PRO GLU VAL GLN ALA GLN ALA TRP SEQRES 14 A 462 GLN ARG LEU GLY ASP ASN PRO ALA SER PRO LEU THR ASN SEQRES 15 A 462 ARG ALA ILE SER GLU THR TYR PRO PRO GLY SER THR PHE SEQRES 16 A 462 LYS VAL ILE THR THR ALA ALA ALA LEU ALA ALA GLY ALA SEQRES 17 A 462 THR GLU THR GLU GLN LEU THR ALA ALA PRO THR ILE PRO SEQRES 18 A 462 LEU PRO GLY SER THR ALA GLN LEU GLU ASN TYR GLY GLY SEQRES 19 A 462 ALA PRO CYS GLY ASP GLU PRO THR VAL SER LEU ARG GLU SEQRES 20 A 462 ALA PHE VAL LYS SER CYS ASN THR ALA PHE VAL GLN LEU SEQRES 21 A 462 GLY ILE ARG THR GLY ALA ASP ALA LEU ARG SER MET ALA SEQRES 22 A 462 ARG ALA PHE GLY LEU ASP SER PRO PRO ARG PRO THR PRO SEQRES 23 A 462 LEU GLN VAL ALA GLU SER THR VAL GLY PRO ILE PRO ASP SEQRES 24 A 462 SER ALA ALA LEU GLY MET THR SER ILE GLY GLN LYS ASP SEQRES 25 A 462 VAL ALA LEU THR PRO LEU ALA ASN ALA GLU ILE ALA ALA SEQRES 26 A 462 THR ILE ALA ASN GLY GLY ILE THR MET ARG PRO TYR LEU SEQRES 27 A 462 VAL GLY SER LEU LYS GLY PRO ASP LEU ALA ASN ILE SER SEQRES 28 A 462 THR THR VAL ARG TYR GLN GLN ARG ARG ALA VAL SER PRO SEQRES 29 A 462 GLN VAL ALA ALA LYS LEU THR GLU LEU MET VAL GLY ALA SEQRES 30 A 462 GLU LYS VAL ALA GLN GLN LYS GLY ALA ILE PRO GLY VAL SEQRES 31 A 462 GLN ILE ALA SER LYS THR GLY THR ALA GLU HIS GLY THR SEQRES 32 A 462 ASP PRO ARG HIS THR PRO PRO HIS ALA TRP TYR ILE ALA SEQRES 33 A 462 PHE ALA PRO ALA GLN ALA PRO LYS VAL ALA VAL ALA VAL SEQRES 34 A 462 LEU VAL GLU ASN GLY ALA ASP ARG LEU SER ALA THR GLY SEQRES 35 A 462 GLY ALA LEU ALA ALA PRO ILE GLY ARG ALA VAL ILE GLU SEQRES 36 A 462 ALA ALA LEU GLN GLY GLU PRO SEQRES 1 B 462 GLY ALA MET GLY SER ARG ALA ASP PRO ARG ASN GLN ARG SEQRES 2 B 462 VAL LEU LEU ASP GLU TYR SER ARG GLN ARG GLY GLN ILE SEQRES 3 B 462 THR ALA GLY GLY GLN LEU LEU ALA TYR SER VAL ALA THR SEQRES 4 B 462 ASP GLY ARG PHE ARG PHE LEU ARG VAL TYR PRO ASN PRO SEQRES 5 B 462 GLU VAL TYR ALA PRO VAL THR GLY PHE TYR SER LEU ARG SEQRES 6 B 462 TYR SER SER THR ALA LEU GLU ARG ALA GLU ASP PRO ILE SEQRES 7 B 462 LEU ASN GLY SER ASP ARG ARG LEU PHE GLY ARG ARG LEU SEQRES 8 B 462 ALA ASP PHE PHE THR GLY ARG ASP PRO ARG GLY GLY ASN SEQRES 9 B 462 VAL ASP THR THR ILE ASN PRO ARG ILE GLN GLN ALA GLY SEQRES 10 B 462 TRP ASP ALA MET GLN GLN GLY CYS TYR GLY PRO CYS LYS SEQRES 11 B 462 GLY ALA VAL VAL ALA LEU GLU PRO SER THR GLY LYS ILE SEQRES 12 B 462 LEU ALA LEU VAL SER SER PRO SER TYR ASP PRO ASN LEU SEQRES 13 B 462 LEU ALA SER HIS ASN PRO GLU VAL GLN ALA GLN ALA TRP SEQRES 14 B 462 GLN ARG LEU GLY ASP ASN PRO ALA SER PRO LEU THR ASN SEQRES 15 B 462 ARG ALA ILE SER GLU THR TYR PRO PRO GLY SER THR PHE SEQRES 16 B 462 LYS VAL ILE THR THR ALA ALA ALA LEU ALA ALA GLY ALA SEQRES 17 B 462 THR GLU THR GLU GLN LEU THR ALA ALA PRO THR ILE PRO SEQRES 18 B 462 LEU PRO GLY SER THR ALA GLN LEU GLU ASN TYR GLY GLY SEQRES 19 B 462 ALA PRO CYS GLY ASP GLU PRO THR VAL SER LEU ARG GLU SEQRES 20 B 462 ALA PHE VAL LYS SER CYS ASN THR ALA PHE VAL GLN LEU SEQRES 21 B 462 GLY ILE ARG THR GLY ALA ASP ALA LEU ARG SER MET ALA SEQRES 22 B 462 ARG ALA PHE GLY LEU ASP SER PRO PRO ARG PRO THR PRO SEQRES 23 B 462 LEU GLN VAL ALA GLU SER THR VAL GLY PRO ILE PRO ASP SEQRES 24 B 462 SER ALA ALA LEU GLY MET THR SER ILE GLY GLN LYS ASP SEQRES 25 B 462 VAL ALA LEU THR PRO LEU ALA ASN ALA GLU ILE ALA ALA SEQRES 26 B 462 THR ILE ALA ASN GLY GLY ILE THR MET ARG PRO TYR LEU SEQRES 27 B 462 VAL GLY SER LEU LYS GLY PRO ASP LEU ALA ASN ILE SER SEQRES 28 B 462 THR THR VAL ARG TYR GLN GLN ARG ARG ALA VAL SER PRO SEQRES 29 B 462 GLN VAL ALA ALA LYS LEU THR GLU LEU MET VAL GLY ALA SEQRES 30 B 462 GLU LYS VAL ALA GLN GLN LYS GLY ALA ILE PRO GLY VAL SEQRES 31 B 462 GLN ILE ALA SER LYS THR GLY THR ALA GLU HIS GLY THR SEQRES 32 B 462 ASP PRO ARG HIS THR PRO PRO HIS ALA TRP TYR ILE ALA SEQRES 33 B 462 PHE ALA PRO ALA GLN ALA PRO LYS VAL ALA VAL ALA VAL SEQRES 34 B 462 LEU VAL GLU ASN GLY ALA ASP ARG LEU SER ALA THR GLY SEQRES 35 B 462 GLY ALA LEU ALA ALA PRO ILE GLY ARG ALA VAL ILE GLU SEQRES 36 B 462 ALA ALA LEU GLN GLY GLU PRO HET CEF A 800 26 HET CEF B 800 26 HETNAM CEF CEFOTAXIME, C3' CLEAVED, OPEN, BOUND FORM FORMUL 3 CEF 2(C14 H15 N5 O5 S2) FORMUL 5 HOH *21(H2 O) HELIX 1 1 ASP A 46 ARG A 50 5 5 HELIX 2 2 ASN A 80 GLY A 89 1 10 HELIX 3 3 THR A 98 GLU A 104 1 7 HELIX 4 4 GLU A 104 GLY A 110 1 7 HELIX 5 5 ASP A 112 ARG A 114 5 3 HELIX 6 6 LEU A 115 GLY A 126 1 12 HELIX 7 7 ASN A 139 GLY A 153 1 15 HELIX 8 8 ASP A 182 ALA A 187 1 6 HELIX 9 9 ASN A 190 ASN A 204 1 15 HELIX 10 10 PRO A 220 THR A 223 5 4 HELIX 11 11 PHE A 224 ALA A 235 1 12 HELIX 12 12 LEU A 274 LYS A 280 1 7 HELIX 13 13 CYS A 282 GLY A 294 1 13 HELIX 14 14 GLY A 294 PHE A 305 1 12 HELIX 15 15 ASP A 328 ILE A 337 1 10 HELIX 16 16 THR A 345 ASN A 358 1 14 HELIX 17 17 SER A 392 ALA A 410 1 19 HELIX 18 18 ASP A 433 THR A 437 5 5 HELIX 19 19 ASN A 462 ARG A 466 5 5 HELIX 20 20 LEU A 474 LEU A 487 1 14 HELIX 21 21 ASN B 80 GLY B 89 1 10 HELIX 22 22 THR B 98 GLU B 104 1 7 HELIX 23 23 GLU B 104 ASN B 109 1 6 HELIX 24 24 ASP B 112 ARG B 114 5 3 HELIX 25 25 LEU B 115 GLY B 126 1 12 HELIX 26 26 ASN B 139 GLY B 153 1 15 HELIX 27 27 PRO B 183 SER B 188 1 6 HELIX 28 28 ASN B 190 ASN B 204 1 15 HELIX 29 29 PRO B 220 THR B 223 5 4 HELIX 30 30 PHE B 224 ALA B 234 1 11 HELIX 31 31 TYR B 261 ALA B 264 5 4 HELIX 32 32 LEU B 274 SER B 281 1 8 HELIX 33 33 CYS B 282 GLY B 294 1 13 HELIX 34 34 GLY B 294 PHE B 305 1 12 HELIX 35 35 ASP B 328 ILE B 337 1 10 HELIX 36 36 THR B 345 ASN B 358 1 14 HELIX 37 37 SER B 392 ALA B 410 1 19 HELIX 38 38 LEU B 474 GLN B 488 1 15 SHEET 1 A 6 PHE A 74 VAL A 77 0 SHEET 2 A 6 GLN A 60 ALA A 67 -1 N TYR A 64 O VAL A 77 SHEET 3 A 6 ILE A 55 ALA A 57 -1 N ILE A 55 O LEU A 62 SHEET 4 A 6 ASN A 133 THR A 136 1 O VAL A 134 N THR A 56 SHEET 5 A 6 VAL A 368 LYS A 372 -1 O SER A 370 N ASP A 135 SHEET 6 A 6 ASN A 378 THR A 381 -1 O SER A 380 N LEU A 371 SHEET 1 B 2 TYR A 91 SER A 92 0 SHEET 2 B 2 SER A 96 SER A 97 -1 O SER A 96 N SER A 92 SHEET 1 C 5 ILE A 172 SER A 178 0 SHEET 2 C 5 GLY A 160 LEU A 165 -1 N GLY A 160 O SER A 178 SHEET 3 C 5 VAL A 454 VAL A 460 -1 O ALA A 455 N LEU A 165 SHEET 4 C 5 HIS A 440 ALA A 447 -1 N ALA A 441 O VAL A 460 SHEET 5 C 5 ALA A 422 ALA A 428 -1 N GLY A 426 O TRP A 442 SHEET 1 D 2 GLN A 242 THR A 244 0 SHEET 2 D 2 THR A 271 SER A 273 -1 O VAL A 272 N LEU A 243 SHEET 1 E 2 THR A 248 PRO A 250 0 SHEET 2 E 2 GLN A 257 GLU A 259 -1 O LEU A 258 N ILE A 249 SHEET 1 F 2 ILE A 361 MET A 363 0 SHEET 2 F 2 GLN A 386 ARG A 389 -1 O ARG A 388 N THR A 362 SHEET 1 G 6 PHE B 74 VAL B 77 0 SHEET 2 G 6 GLN B 60 ALA B 67 -1 N TYR B 64 O VAL B 77 SHEET 3 G 6 ILE B 55 ALA B 57 -1 N ILE B 55 O LEU B 62 SHEET 4 G 6 ASN B 133 THR B 136 1 O THR B 136 N THR B 56 SHEET 5 G 6 VAL B 368 LYS B 372 -1 O SER B 370 N ASP B 135 SHEET 6 G 6 ASN B 378 THR B 381 -1 O SER B 380 N LEU B 371 SHEET 1 H 2 TYR B 91 SER B 92 0 SHEET 2 H 2 SER B 96 SER B 97 -1 O SER B 96 N SER B 92 SHEET 1 I 5 ILE B 172 SER B 178 0 SHEET 2 I 5 GLY B 160 LEU B 165 -1 N GLY B 160 O SER B 178 SHEET 3 I 5 VAL B 454 VAL B 460 -1 O ALA B 455 N LEU B 165 SHEET 4 I 5 HIS B 440 ALA B 447 -1 N TYR B 443 O VAL B 458 SHEET 5 I 5 ALA B 422 ALA B 428 -1 N GLY B 426 O TRP B 442 SHEET 1 J 2 GLN B 242 THR B 244 0 SHEET 2 J 2 THR B 271 SER B 273 -1 O VAL B 272 N LEU B 243 SHEET 1 K 2 THR B 248 PRO B 250 0 SHEET 2 K 2 GLN B 257 GLU B 259 -1 O LEU B 258 N ILE B 249 SHEET 1 L 2 ILE B 361 MET B 363 0 SHEET 2 L 2 GLN B 386 ARG B 389 -1 O GLN B 387 N THR B 362 SSBOND 1 CYS A 154 CYS A 158 1555 1555 2.03 SSBOND 2 CYS A 266 CYS A 282 1555 1555 2.04 SSBOND 3 CYS B 154 CYS B 158 1555 1555 2.05 SSBOND 4 CYS B 266 CYS B 282 1555 1555 2.04 LINK OG SER A 222 C8 CEF A 800 1555 1555 1.38 LINK OG SER B 222 C8 CEF B 800 1555 1555 1.37 CISPEP 1 SER A 178 PRO A 179 0 -3.95 CISPEP 2 TYR A 261 GLY A 262 0 -23.67 CISPEP 3 THR A 314 PRO A 315 0 10.24 CISPEP 4 ALA A 447 PRO A 448 0 -13.21 CISPEP 5 SER B 178 PRO B 179 0 3.32 CISPEP 6 THR B 314 PRO B 315 0 9.26 CISPEP 7 ALA B 447 PRO B 448 0 -13.57 SITE 1 AC1 11 GLY A 221 SER A 222 TYR A 261 SER A 281 SITE 2 AC1 11 ASN A 283 GLN A 339 LYS A 424 THR A 425 SITE 3 AC1 11 GLY A 426 THR A 427 THR A 470 SITE 1 AC2 12 SER B 222 TYR B 261 SER B 281 ASN B 283 SITE 2 AC2 12 THR B 425 GLY B 426 THR B 427 GLU B 429 SITE 3 AC2 12 SER B 468 ALA B 469 GLY B 471 GLY B 472 CRYST1 123.078 123.078 101.284 90.00 90.00 120.00 P 61 12 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 0.008125 0.004691 0.000000 0.00000 SCALE2 0.000000 0.009382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009873 0.00000