HEADER HYDROLASE/ANTIBIOTIC 21-OCT-13 4N9K TITLE CRYSTAL STRUCTURE OF BETA-LACTAMSE PENP_E166S IN COMPLEX WITH TITLE 2 CEPHALORIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: SMALL EXOPENICILLINASE; COMPND 5 SYNONYM: PENICILLINASE; COMPND 6 EC: 3.5.2.6; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 GENE: BLAP, PENP, PENP BLAP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS HYDROLASE, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.PAN,W.WONG,Y.ZHAO REVDAT 1 10-SEP-14 4N9K 0 JRNL AUTH X.PAN,W.WONG,Y.HE,Y.JIANG,Y.ZHAO JRNL TITL PERTURBING THE GENERAL BASE RESIDUE GLU166 IN THE ACTIVE JRNL TITL 2 SITE OF CLASS A BETA-LACTAMASE LEADS TO ENHANCED CARBAPENEM JRNL TITL 3 BINDING AND ACYLATION JRNL REF BIOCHEMISTRY V. 53 5414 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 25020031 JRNL DOI 10.1021/BI401609H REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 31753 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1617 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2037 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 411 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : -0.01000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : 0.01000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.816 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4228 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4155 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5742 ; 1.992 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9602 ; 0.988 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 7.047 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;35.958 ;25.179 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 781 ;15.518 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.183 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 669 ; 0.210 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4765 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 891 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2080 ; 1.255 ; 1.333 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2079 ; 1.242 ; 1.331 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2591 ; 1.937 ; 1.985 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4N9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-NOV-13. REMARK 100 THE RCSB ID CODE IS RCSB082923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX SYSTEM BY OSMIC REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DTREK REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31754 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 42.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, PEG 3350, AMMONIUM ACETATE, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B 23 REMARK 465 PRO B 24 REMARK 465 MET B 25 REMARK 465 LYS B 26 REMARK 465 THR B 27 REMARK 465 GLU B 28 REMARK 465 MET B 29 REMARK 465 LYS B 30 REMARK 465 MET B 292 REMARK 465 ASN B 293 REMARK 465 GLY B 294 REMARK 465 LYS B 295 REMARK 465 GLY A 23 REMARK 465 PRO A 24 REMARK 465 MET A 25 REMARK 465 LYS A 26 REMARK 465 THR A 27 REMARK 465 GLU A 28 REMARK 465 MET A 29 REMARK 465 LYS A 30 REMARK 465 MET A 292 REMARK 465 ASN A 293 REMARK 465 GLY A 294 REMARK 465 LYS A 295 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 OE1 GLU A 202 O HOH A 500 1.73 REMARK 500 O HOH B 573 O HOH B 643 1.89 REMARK 500 O HOH B 498 O HOH B 558 2.01 REMARK 500 OD2 ASP B 50 O HOH B 571 2.08 REMARK 500 OD1 ASP B 31 O HOH B 471 2.08 REMARK 500 OE1 GLN B 83 O HOH B 574 2.10 REMARK 500 O ALA B 238 O HOH B 446 2.12 REMARK 500 CB ASP A 268 O HOH A 442 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 140 CD PRO A 254 1545 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL B 57 C ALA B 59 N 0.235 REMARK 500 GLN B 83 C LYS B 86 N 0.286 REMARK 500 ALA B 238 C SER B 240 N 0.247 REMARK 500 PRO B 252 C PRO B 254 N 0.206 REMARK 500 VAL A 57 C ALA A 59 N 0.150 REMARK 500 ALA A 238 C SER A 240 N 0.145 REMARK 500 PRO A 252 C PRO A 254 N 0.215 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP B 41 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG B 65 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 GLN B 83 O - C - N ANGL. DEV. = -10.6 DEGREES REMARK 500 ARG B 128 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 184 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG B 184 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 65 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 GLN A 83 O - C - N ANGL. DEV. = -12.3 DEGREES REMARK 500 LYS A 86 C - N - CA ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 184 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 204 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 204 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 213 NE - CZ - NH1 ANGL. DEV. = 3.2 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 ASP B 41 60.49 39.66 REMARK 500 ALA B 69 -139.61 46.20 REMARK 500 VAL B 103 -135.06 -127.95 REMARK 500 GLU B 163 -37.41 -134.02 REMARK 500 GLU B 196 -137.35 -110.49 REMARK 500 LEU B 220 -118.50 -112.38 REMARK 500 ALA A 69 -146.03 58.04 REMARK 500 VAL A 103 -134.21 -127.16 REMARK 500 ASN A 106 53.61 -143.39 REMARK 500 GLU A 196 -137.23 -106.64 REMARK 500 LEU A 220 -115.92 -108.50 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 PRO A 252 PRO A 254 -146.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 VAL B 57 19.73 REMARK 500 PRO A 252 14.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP B 268 24.8 L L OUTSIDE RANGE REMARK 500 ASP A 268 23.6 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CED B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CED A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N92 RELATED DB: PDB REMARK 900 RELATED ID: 4N9L RELATED DB: PDB DBREF 4N9K B 26 295 UNP P00808 BLAC_BACLI 43 307 DBREF 4N9K A 26 295 UNP P00808 BLAC_BACLI 43 307 SEQADV 4N9K GLY B 23 UNP P00808 EXPRESSION TAG SEQADV 4N9K PRO B 24 UNP P00808 EXPRESSION TAG SEQADV 4N9K MET B 25 UNP P00808 EXPRESSION TAG SEQADV 4N9K SER B 166 UNP P00808 GLU 180 ENGINEERED MUTATION SEQADV 4N9K GLY A 23 UNP P00808 EXPRESSION TAG SEQADV 4N9K PRO A 24 UNP P00808 EXPRESSION TAG SEQADV 4N9K MET A 25 UNP P00808 EXPRESSION TAG SEQADV 4N9K SER A 166 UNP P00808 GLU 180 ENGINEERED MUTATION SEQRES 1 B 268 GLY PRO MET LYS THR GLU MET LYS ASP ASP PHE ALA LYS SEQRES 2 B 268 LEU GLU GLU GLN PHE ASP ALA LYS LEU GLY ILE PHE ALA SEQRES 3 B 268 LEU ASP THR GLY THR ASN ARG THR VAL ALA TYR ARG PRO SEQRES 4 B 268 ASP GLU ARG PHE ALA PHE ALA SER THR ILE LYS ALA LEU SEQRES 5 B 268 THR VAL GLY VAL LEU LEU GLN GLN LYS SER ILE GLU ASP SEQRES 6 B 268 LEU ASN GLN ARG ILE THR TYR THR ARG ASP ASP LEU VAL SEQRES 7 B 268 ASN TYR ASN PRO ILE THR GLU LYS HIS VAL ASP THR GLY SEQRES 8 B 268 MET THR LEU LYS GLU LEU ALA ASP ALA SER LEU ARG TYR SEQRES 9 B 268 SER ASP ASN ALA ALA GLN ASN LEU ILE LEU LYS GLN ILE SEQRES 10 B 268 GLY GLY PRO GLU SER LEU LYS LYS GLU LEU ARG LYS ILE SEQRES 11 B 268 GLY ASP GLU VAL THR ASN PRO GLU ARG PHE SER PRO GLU SEQRES 12 B 268 LEU ASN GLU VAL ASN PRO GLY GLU THR GLN ASP THR SER SEQRES 13 B 268 THR ALA ARG ALA LEU VAL THR SER LEU ARG ALA PHE ALA SEQRES 14 B 268 LEU GLU ASP LYS LEU PRO SER GLU LYS ARG GLU LEU LEU SEQRES 15 B 268 ILE ASP TRP MET LYS ARG ASN THR THR GLY ASP ALA LEU SEQRES 16 B 268 ILE ARG ALA GLY VAL PRO ASP GLY TRP GLU VAL ALA ASP SEQRES 17 B 268 LYS THR GLY ALA ALA SER TYR GLY THR ARG ASN ASP ILE SEQRES 18 B 268 ALA ILE ILE TRP PRO PRO LYS GLY ASP PRO VAL VAL LEU SEQRES 19 B 268 ALA VAL LEU SER SER ARG ASP LYS LYS ASP ALA LYS TYR SEQRES 20 B 268 ASP ASP LYS LEU ILE ALA GLU ALA THR LYS VAL VAL MET SEQRES 21 B 268 LYS ALA LEU ASN MET ASN GLY LYS SEQRES 1 A 268 GLY PRO MET LYS THR GLU MET LYS ASP ASP PHE ALA LYS SEQRES 2 A 268 LEU GLU GLU GLN PHE ASP ALA LYS LEU GLY ILE PHE ALA SEQRES 3 A 268 LEU ASP THR GLY THR ASN ARG THR VAL ALA TYR ARG PRO SEQRES 4 A 268 ASP GLU ARG PHE ALA PHE ALA SER THR ILE LYS ALA LEU SEQRES 5 A 268 THR VAL GLY VAL LEU LEU GLN GLN LYS SER ILE GLU ASP SEQRES 6 A 268 LEU ASN GLN ARG ILE THR TYR THR ARG ASP ASP LEU VAL SEQRES 7 A 268 ASN TYR ASN PRO ILE THR GLU LYS HIS VAL ASP THR GLY SEQRES 8 A 268 MET THR LEU LYS GLU LEU ALA ASP ALA SER LEU ARG TYR SEQRES 9 A 268 SER ASP ASN ALA ALA GLN ASN LEU ILE LEU LYS GLN ILE SEQRES 10 A 268 GLY GLY PRO GLU SER LEU LYS LYS GLU LEU ARG LYS ILE SEQRES 11 A 268 GLY ASP GLU VAL THR ASN PRO GLU ARG PHE SER PRO GLU SEQRES 12 A 268 LEU ASN GLU VAL ASN PRO GLY GLU THR GLN ASP THR SER SEQRES 13 A 268 THR ALA ARG ALA LEU VAL THR SER LEU ARG ALA PHE ALA SEQRES 14 A 268 LEU GLU ASP LYS LEU PRO SER GLU LYS ARG GLU LEU LEU SEQRES 15 A 268 ILE ASP TRP MET LYS ARG ASN THR THR GLY ASP ALA LEU SEQRES 16 A 268 ILE ARG ALA GLY VAL PRO ASP GLY TRP GLU VAL ALA ASP SEQRES 17 A 268 LYS THR GLY ALA ALA SER TYR GLY THR ARG ASN ASP ILE SEQRES 18 A 268 ALA ILE ILE TRP PRO PRO LYS GLY ASP PRO VAL VAL LEU SEQRES 19 A 268 ALA VAL LEU SER SER ARG ASP LYS LYS ASP ALA LYS TYR SEQRES 20 A 268 ASP ASP LYS LEU ILE ALA GLU ALA THR LYS VAL VAL MET SEQRES 21 A 268 LYS ALA LEU ASN MET ASN GLY LYS HET CED B 301 22 HET CED A 301 22 HETNAM CED 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)- HETNAM 2 CED ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID HETSYN CED DEGRADED CEPHALORIDINE, OPEN FORM FORMUL 3 CED 2(C14 H16 N2 O4 S2) FORMUL 5 HOH *411(H2 O) HELIX 1 1 ASP B 31 ASP B 41 1 11 HELIX 2 2 THR B 71 LYS B 86 1 14 HELIX 3 3 ILE B 88 ASN B 92 5 5 HELIX 4 4 THR B 98 LEU B 102 5 5 HELIX 5 5 ILE B 108 HIS B 112 5 5 HELIX 6 6 LEU B 119 SER B 130 1 12 HELIX 7 7 ASP B 131 GLY B 143 1 13 HELIX 8 8 GLY B 143 GLY B 156 1 14 HELIX 9 9 PRO B 167 GLU B 171 5 5 HELIX 10 10 THR B 182 LEU B 195 1 14 HELIX 11 11 PRO B 200 ARG B 213 1 14 HELIX 12 12 LEU B 220 VAL B 225 5 6 HELIX 13 13 ASP B 276 ASN B 291 1 16 HELIX 14 14 ASP A 32 ASP A 41 1 10 HELIX 15 15 THR A 71 LYS A 86 1 14 HELIX 16 16 ILE A 88 ASN A 92 5 5 HELIX 17 17 THR A 98 LEU A 102 5 5 HELIX 18 18 ILE A 108 HIS A 112 5 5 HELIX 19 19 LEU A 119 SER A 130 1 12 HELIX 20 20 ASP A 131 ILE A 142 1 12 HELIX 21 21 GLY A 143 GLY A 156 1 14 HELIX 22 22 PRO A 167 GLU A 171 5 5 HELIX 23 23 THR A 182 GLU A 196 1 15 HELIX 24 24 PRO A 200 ARG A 213 1 14 HELIX 25 25 LEU A 220 VAL A 225 5 6 HELIX 26 26 ASP A 276 LEU A 290 1 15 SHEET 1 A 5 ARG B 55 TYR B 60 0 SHEET 2 A 5 LYS B 43 ASP B 50 -1 N ILE B 46 O TYR B 60 SHEET 3 A 5 VAL B 259 SER B 266 -1 O LEU B 264 N GLY B 45 SHEET 4 A 5 THR B 243 TRP B 251 -1 N ILE B 250 O VAL B 259 SHEET 5 A 5 GLU B 230 ALA B 238 -1 N GLU B 230 O TRP B 251 SHEET 1 B 2 PHE B 66 ALA B 67 0 SHEET 2 B 2 THR B 180 SER B 181 -1 O SER B 181 N PHE B 66 SHEET 1 C 2 ARG B 94 ILE B 95 0 SHEET 2 C 2 MET B 117 THR B 118 -1 O MET B 117 N ILE B 95 SHEET 1 D 5 THR A 56 TYR A 60 0 SHEET 2 D 5 LYS A 43 ASP A 50 -1 N ILE A 46 O TYR A 60 SHEET 3 D 5 VAL A 259 SER A 266 -1 O LEU A 264 N GLY A 45 SHEET 4 D 5 THR A 243 TRP A 251 -1 N ALA A 248 O LEU A 261 SHEET 5 D 5 GLU A 230 ALA A 238 -1 N ALA A 232 O ILE A 249 SHEET 1 E 2 PHE A 66 ALA A 67 0 SHEET 2 E 2 THR A 180 SER A 181 -1 O SER A 181 N PHE A 66 SHEET 1 F 2 ARG A 94 ILE A 95 0 SHEET 2 F 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 LINK OG SER B 70 C8 CED B 301 1555 1555 1.56 LINK OG SER A 70 C8 CED A 301 1555 1555 1.65 CISPEP 1 SER B 166 PRO B 167 0 4.64 CISPEP 2 SER A 166 PRO A 167 0 7.25 SITE 1 AC1 14 ASP A 114 ALA B 69 SER B 70 ASN B 104 SITE 2 AC1 14 TYR B 105 SER B 130 ASN B 132 ASN B 170 SITE 3 AC1 14 LYS B 234 THR B 235 GLY B 236 ALA B 237 SITE 4 AC1 14 ARG B 244 HOH B 523 SITE 1 AC2 13 ALA A 69 SER A 70 ASN A 104 TYR A 105 SITE 2 AC2 13 SER A 130 ASN A 132 ASN A 170 LYS A 234 SITE 3 AC2 13 THR A 235 GLY A 236 ALA A 237 ARG A 244 SITE 4 AC2 13 HOH A 456 CRYST1 43.370 45.800 66.120 77.85 75.41 69.00 P 1 2 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 0.023057 -0.008851 -0.004867 0.00000 SCALE2 0.000000 0.023387 -0.003139 0.00000 SCALE3 0.000000 0.000000 0.015768 0.00000