HEADER HYDROLASE/ANTIBIOTIC 29-OCT-09 3KGO OBSLTE 27-JUL-11 3KGO 3SH8 TITLE CRYSTAL STRUCTURE OF FLUOROPHORE-LABELED CLASS A BETA-LACTAMASE PENP TITLE 2 IN COMPLEX WITH CEPHALORIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 47-304; COMPND 5 SYNONYM: PENICILLINASE, LARGE EXOPENICILLINASE, SMALL COMPND 6 EXOPENICILLINASE; COMPND 7 EC: 3.5.2.6; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 STRAIN: 749/C; SOURCE 5 GENE: BLAP, PENP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET-K KEYWDS BETA-LACTAMASE, FLUOROPHORE, BIOSENSOR, CEPHALORIDINE, ANTIBIOTIC KEYWDS 2 RESISTANCE, CELL MEMBRANE, LIPOPROTEIN, MEMBRANE, PALMITATE, KEYWDS 3 HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.T.WONG REVDAT 2 27-JUL-11 3KGO 1 OBSLTE REVDAT 1 08-DEC-10 3KGO 0 JRNL AUTH W.T.WONG JRNL TITL CRYSTAL STRUCTURE OF FLUOROPHORE-LABELED CLASS A JRNL TITL 2 BETA-LACTAMASE PENP IN COMPLEX WITH CEPHALORIDINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 31835 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1752 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2349 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3941 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 346 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.212 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.132 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.660 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4043 ; 0.032 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5455 ; 2.884 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 493 ;10.169 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;36.788 ;24.835 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 728 ;18.955 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;20.269 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 630 ; 0.260 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2986 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2071 ; 0.272 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2730 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 354 ; 0.234 ; 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): 53 ; 0.230 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.167 ; 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): 2599 ; 1.294 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4035 ; 2.118 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1644 ; 2.965 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1420 ; 4.583 ; 4.500 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 3KGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB055969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 7.5 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46065 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 64.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 7.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 45.86500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 LEU A 169 REMARK 465 ASN A 170 REMARK 465 GLU A 171 REMARK 465 VAL A 172 REMARK 465 MET A 292 REMARK 465 LYS B 30 REMARK 465 LEU B 169 REMARK 465 ASN B 170 REMARK 465 GLU B 171 REMARK 465 VAL B 172 REMARK 465 MET B 292 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 30 CG CD CE NZ 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 CA ASN B 291 O HOH B 353 1.18 REMARK 500 O4B CED B 1 O HOH B 4 1.32 REMARK 500 N ASN B 291 O HOH B 353 1.51 REMARK 500 C4' CED B 1 O HOH B 4 1.60 REMARK 500 OG SER B 70 C8 CED B 1 1.69 REMARK 500 O4A CED B 1 O HOH B 4 1.82 REMARK 500 O HOH B 372 O HOH B 375 1.88 REMARK 500 O SER B 130 O HOH B 308 1.93 REMARK 500 O9 CED B 1 O HOH B 336 1.94 REMARK 500 O HOH A 294 O HOH A 462 1.97 REMARK 500 NZ LYS A 198 O HOH A 439 1.98 REMARK 500 OG SER A 70 C7 CED A 1 2.07 REMARK 500 OD1 ASN B 132 O HOH B 308 2.09 REMARK 500 O HOH A 355 O HOH A 411 2.18 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 A 57 C ALA A 59 N 0.156 REMARK 500 GLN A 83 C LYS A 86 N 0.227 REMARK 500 GLU A 205 CG GLU A 205 CD 0.098 REMARK 500 ALA A 238 C SER A 240 N 0.238 REMARK 500 PRO A 252 C PRO A 254 N 0.233 REMARK 500 VAL B 57 C ALA B 59 N 0.215 REMARK 500 GLN B 83 C LYS B 86 N 0.176 REMARK 500 GLU B 158 CB GLU B 158 CG 0.135 REMARK 500 ALA B 238 C SER B 240 N 0.258 REMARK 500 PRO B 252 C PRO B 254 N 0.222 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 GLN A 83 CA - C - N ANGL. DEV. = 21.6 DEGREES REMARK 500 GLN A 83 O - C - N ANGL. DEV. = -24.5 DEGREES REMARK 500 LYS A 86 C - N - CA ANGL. DEV. = 19.8 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 179 N - CA - C ANGL. DEV. = -20.0 DEGREES REMARK 500 ARG A 213 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 213 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ALA A 238 O - C - N ANGL. DEV. = -10.3 DEGREES REMARK 500 PRO A 252 O - C - N ANGL. DEV. = -11.6 DEGREES REMARK 500 GLN B 83 O - C - N ANGL. DEV. = -12.6 DEGREES REMARK 500 ALA B 238 CA - C - N ANGL. DEV. = 17.4 DEGREES REMARK 500 ALA B 238 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 PRO B 252 O - C - N ANGL. DEV. = -20.1 DEGREES REMARK 500 PRO B 254 C - N - CD ANGL. DEV. = -20.4 DEGREES REMARK 500 PRO B 254 O - C - N ANGL. DEV. = -10.0 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 ALA A 69 -141.04 49.79 REMARK 500 VAL A 103 -137.68 -121.94 REMARK 500 GLU A 163 -34.03 -135.53 REMARK 500 CYS A 166 -21.92 104.09 REMARK 500 ASP A 179 35.30 102.10 REMARK 500 GLU A 196 -129.06 -110.05 REMARK 500 LEU A 220 -122.83 -105.32 REMARK 500 SER A 240 174.36 -42.25 REMARK 500 PRO A 254 -52.97 -23.28 REMARK 500 ALA B 69 -139.40 48.01 REMARK 500 VAL B 103 -138.24 -120.13 REMARK 500 CYS B 166 111.15 54.97 REMARK 500 PRO B 167 -135.73 21.35 REMARK 500 PRO B 174 -151.99 -78.88 REMARK 500 GLU B 196 -144.32 -100.08 REMARK 500 LEU B 220 -127.93 -108.53 REMARK 500 SER B 240 151.41 3.70 REMARK 500 PRO B 254 -95.87 7.17 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 CYS A 166 PRO A 167 -46.06 REMARK 500 GLN A 178 ASP A 179 124.57 REMARK 500 CYS B 166 PRO B 167 74.94 REMARK 500 PRO B 167 GLU B 168 -44.43 REMARK 500 ALA B 238 SER B 240 141.44 REMARK 500 LEU B 290 ASN B 291 96.29 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 ALA A 238 19.51 REMARK 500 PRO A 252 11.37 REMARK 500 VAL B 57 20.20 REMARK 500 PRO B 252 28.26 REMARK 500 PRO B 254 15.14 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 VAL A 159 23.7 L L OUTSIDE RANGE REMARK 500 CYS A 166 21.9 L L OUTSIDE RANGE REMARK 500 VAL A 187 22.7 L L OUTSIDE RANGE REMARK 500 VAL A 260 23.8 L L OUTSIDE RANGE REMARK 500 VAL B 187 24.2 L L OUTSIDE RANGE REMARK 500 VAL B 260 24.2 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 396 DISTANCE = 6.12 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CED A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CED B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KGM RELATED DB: PDB REMARK 900 RELATED ID: 3KGN RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE NUMBERS 58, 84, 85, 239, 253 ARE SIMPLY SKIPPED DBREF 3KGO A 30 292 UNP P00808 BLAC_BACLI 47 304 DBREF 3KGO B 30 292 UNP P00808 BLAC_BACLI 47 304 SEQADV 3KGO CYS A 166 UNP P00808 GLU 180 ENGINEERED SEQADV 3KGO CYS B 166 UNP P00808 GLU 180 ENGINEERED SEQRES 1 A 258 LYS ASP ASP PHE ALA LYS LEU GLU GLU GLN PHE ASP ALA SEQRES 2 A 258 LYS LEU GLY ILE PHE ALA LEU ASP THR GLY THR ASN ARG SEQRES 3 A 258 THR VAL ALA TYR ARG PRO ASP GLU ARG PHE ALA PHE ALA SEQRES 4 A 258 SER THR ILE LYS ALA LEU THR VAL GLY VAL LEU LEU GLN SEQRES 5 A 258 GLN LYS SER ILE GLU ASP LEU ASN GLN ARG ILE THR TYR SEQRES 6 A 258 THR ARG ASP ASP LEU VAL ASN TYR ASN PRO ILE THR GLU SEQRES 7 A 258 LYS HIS VAL ASP THR GLY MET THR LEU LYS GLU LEU ALA SEQRES 8 A 258 ASP ALA SER LEU ARG TYR SER ASP ASN ALA ALA GLN ASN SEQRES 9 A 258 LEU ILE LEU LYS GLN ILE GLY GLY PRO GLU SER LEU LYS SEQRES 10 A 258 LYS GLU LEU ARG LYS ILE GLY ASP GLU VAL THR ASN PRO SEQRES 11 A 258 GLU ARG PHE CYS PRO GLU LEU ASN GLU VAL ASN PRO GLY SEQRES 12 A 258 GLU THR GLN ASP THR SER THR ALA ARG ALA LEU VAL THR SEQRES 13 A 258 SER LEU ARG ALA PHE ALA LEU GLU ASP LYS LEU PRO SER SEQRES 14 A 258 GLU LYS ARG GLU LEU LEU ILE ASP TRP MET LYS ARG ASN SEQRES 15 A 258 THR THR GLY ASP ALA LEU ILE ARG ALA GLY VAL PRO ASP SEQRES 16 A 258 GLY TRP GLU VAL ALA ASP LYS THR GLY ALA ALA SER TYR SEQRES 17 A 258 GLY THR ARG ASN ASP ILE ALA ILE ILE TRP PRO PRO LYS SEQRES 18 A 258 GLY ASP PRO VAL VAL LEU ALA VAL LEU SER SER ARG ASP SEQRES 19 A 258 LYS LYS ASP ALA LYS TYR ASP ASP LYS LEU ILE ALA GLU SEQRES 20 A 258 ALA THR LYS VAL VAL MET LYS ALA LEU ASN MET SEQRES 1 B 258 LYS ASP ASP PHE ALA LYS LEU GLU GLU GLN PHE ASP ALA SEQRES 2 B 258 LYS LEU GLY ILE PHE ALA LEU ASP THR GLY THR ASN ARG SEQRES 3 B 258 THR VAL ALA TYR ARG PRO ASP GLU ARG PHE ALA PHE ALA SEQRES 4 B 258 SER THR ILE LYS ALA LEU THR VAL GLY VAL LEU LEU GLN SEQRES 5 B 258 GLN LYS SER ILE GLU ASP LEU ASN GLN ARG ILE THR TYR SEQRES 6 B 258 THR ARG ASP ASP LEU VAL ASN TYR ASN PRO ILE THR GLU SEQRES 7 B 258 LYS HIS VAL ASP THR GLY MET THR LEU LYS GLU LEU ALA SEQRES 8 B 258 ASP ALA SER LEU ARG TYR SER ASP ASN ALA ALA GLN ASN SEQRES 9 B 258 LEU ILE LEU LYS GLN ILE GLY GLY PRO GLU SER LEU LYS SEQRES 10 B 258 LYS GLU LEU ARG LYS ILE GLY ASP GLU VAL THR ASN PRO SEQRES 11 B 258 GLU ARG PHE CYS PRO GLU LEU ASN GLU VAL ASN PRO GLY SEQRES 12 B 258 GLU THR GLN ASP THR SER THR ALA ARG ALA LEU VAL THR SEQRES 13 B 258 SER LEU ARG ALA PHE ALA LEU GLU ASP LYS LEU PRO SER SEQRES 14 B 258 GLU LYS ARG GLU LEU LEU ILE ASP TRP MET LYS ARG ASN SEQRES 15 B 258 THR THR GLY ASP ALA LEU ILE ARG ALA GLY VAL PRO ASP SEQRES 16 B 258 GLY TRP GLU VAL ALA ASP LYS THR GLY ALA ALA SER TYR SEQRES 17 B 258 GLY THR ARG ASN ASP ILE ALA ILE ILE TRP PRO PRO LYS SEQRES 18 B 258 GLY ASP PRO VAL VAL LEU ALA VAL LEU SER SER ARG ASP SEQRES 19 B 258 LYS LYS ASP ALA LYS TYR ASP ASP LYS LEU ILE ALA GLU SEQRES 20 B 258 ALA THR LYS VAL VAL MET LYS ALA LEU ASN MET HET CED A 1 22 HET CED B 1 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 FORMUL 3 CED 2(C14 H16 N2 O4 S2) FORMUL 5 HOH *346(H2 O) HELIX 1 1 LYS A 30 ASP A 41 1 12 HELIX 2 2 THR A 71 LYS A 86 1 14 HELIX 3 3 ILE A 88 ASN A 92 5 5 HELIX 4 4 THR A 98 LEU A 102 5 5 HELIX 5 5 ILE A 108 VAL A 113 5 6 HELIX 6 6 LEU A 119 SER A 130 1 12 HELIX 7 7 ASP A 131 ILE A 142 1 12 HELIX 8 8 GLY A 144 ILE A 155 1 12 HELIX 9 9 THR A 182 LEU A 195 1 14 HELIX 10 10 PRO A 200 ARG A 213 1 14 HELIX 11 11 LEU A 220 VAL A 225 5 6 HELIX 12 12 ASP A 275 ASN A 291 1 17 HELIX 13 13 ASP B 31 ASP B 41 1 11 HELIX 14 14 THR B 71 LYS B 86 1 14 HELIX 15 15 GLU B 89 ASN B 92 5 4 HELIX 16 16 THR B 98 LEU B 102 5 5 HELIX 17 17 ILE B 108 HIS B 112 5 5 HELIX 18 18 LEU B 119 SER B 130 1 12 HELIX 19 19 ASP B 131 GLY B 143 1 13 HELIX 20 20 GLY B 144 ILE B 155 1 12 HELIX 21 21 THR B 182 LEU B 195 1 14 HELIX 22 22 PRO B 200 ARG B 213 1 14 HELIX 23 23 LEU B 220 VAL B 225 5 6 HELIX 24 24 ASP B 276 ASN B 291 1 16 SHEET 1 A 5 THR A 56 TYR A 60 0 SHEET 2 A 5 LYS A 43 ASP A 50 -1 N ILE A 46 O TYR A 60 SHEET 3 A 5 VAL A 259 SER A 266 -1 O LEU A 264 N GLY A 45 SHEET 4 A 5 THR A 243 TRP A 251 -1 N ILE A 250 O VAL A 259 SHEET 5 A 5 GLU A 230 ALA A 238 -1 N GLU A 230 O TRP A 251 SHEET 1 B 2 PHE A 66 ALA A 67 0 SHEET 2 B 2 THR A 180 SER A 181 -1 O SER A 181 N PHE A 66 SHEET 1 C 2 ARG A 94 ILE A 95 0 SHEET 2 C 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 SHEET 1 D 5 THR B 56 TYR B 60 0 SHEET 2 D 5 LYS B 43 ASP B 50 -1 N ILE B 46 O TYR B 60 SHEET 3 D 5 VAL B 259 SER B 266 -1 O SER B 266 N LYS B 43 SHEET 4 D 5 THR B 243 TRP B 251 -1 N ASP B 246 O VAL B 263 SHEET 5 D 5 GLU B 230 ALA B 238 -1 N GLU B 230 O TRP B 251 SHEET 1 E 2 PHE B 66 ALA B 67 0 SHEET 2 E 2 THR B 180 SER B 181 -1 O SER B 181 N PHE B 66 SHEET 1 F 2 ARG B 94 ILE B 95 0 SHEET 2 F 2 MET B 117 THR B 118 -1 O MET B 117 N ILE B 95 CISPEP 1 PRO A 167 GLU A 168 0 -14.50 CISPEP 2 PRO A 174 GLY A 175 0 -16.04 CISPEP 3 ASN B 173 PRO B 174 0 -9.60 SITE 1 AC1 12 ALA A 69 SER A 70 ASN A 104 SER A 130 SITE 2 AC1 12 ASN A 132 GLU A 168 LYS A 234 THR A 235 SITE 3 AC1 12 GLY A 236 ALA A 237 ARG A 244 HOH A 396 SITE 1 AC2 14 HOH B 4 ALA B 69 SER B 70 ASN B 104 SITE 2 AC2 14 SER B 130 ASN B 132 GLU B 168 THR B 235 SITE 3 AC2 14 GLY B 236 ALA B 237 ARG B 244 HOH B 308 SITE 4 AC2 14 HOH B 336 HOH B 415 CRYST1 43.330 91.730 66.110 90.00 104.00 90.00 P 1 21 1 4 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 0.023079 0.000000 0.005754 0.00000 SCALE2 0.000000 0.010902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015589 0.00000