HEADER HYDROLASE 07-MAR-18 5ZG6 TITLE CRYSTAL STRUCTURE OF BETA-LACTAMASE PENP MUTANT-E166Y IN COMPLEX WITH TITLE 2 CEPHALORIDINE AS "POST-ACYLATION" INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: PENICILLINASE; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 GENE: PENP, BLAP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS CLASS A BETA-LACTAMASE, ANTIBIOTIC RESISTANCE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.PAN,Y.ZHAO REVDAT 3 22-NOV-23 5ZG6 1 REMARK REVDAT 2 08-JUL-20 5ZG6 1 JRNL REVDAT 1 20-MAR-19 5ZG6 0 JRNL AUTH Y.HE,J.LEI,X.PAN,X.HUANG,Y.ZHAO JRNL TITL THE HYDROLYTIC WATER MOLECULE OF CLASS A BETA-LACTAMASE JRNL TITL 2 RELIES ON THE ACYL-ENZYME INTERMEDIATE ES* FOR PROPER JRNL TITL 3 COORDINATION AND CATALYSIS. JRNL REF SCI REP V. 10 10205 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32576842 JRNL DOI 10.1038/S41598-020-66431-W REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 27895 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1486 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) : 1999 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.88 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) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.263 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.207 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4114 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3936 ; 0.035 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5554 ; 1.552 ; 1.657 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9130 ; 2.393 ; 1.590 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 502 ; 7.554 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;31.334 ;22.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 740 ;16.268 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;18.882 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4560 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 810 ; 0.011 ; 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): 2038 ; 1.346 ; 1.696 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2037 ; 1.346 ; 1.695 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2530 ; 2.163 ; 2.530 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2531 ; 2.163 ; 2.532 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2076 ; 1.674 ; 1.925 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2077 ; 1.674 ; 1.925 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3025 ; 2.750 ; 2.809 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4506 ; 4.389 ;19.851 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4501 ; 4.385 ;19.849 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 5ZG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300007020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29472 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 63.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.31300 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: 4BLM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH8.0, 25% PEG 3350, 0.4M REMARK 280 AMMONIUM ACETATE, 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, 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 OG SER B 70 O9 CED B 301 2.16 REMARK 500 OG SER A 70 O9 CED A 301 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 B 57 C ALA B 59 N 0.264 REMARK 500 GLN B 83 C LYS B 86 N 0.215 REMARK 500 PRO B 252 C PRO B 254 N 0.194 REMARK 500 ALA A 238 C SER A 240 N 0.205 REMARK 500 PRO A 252 C PRO A 254 N 0.183 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 PRO B 252 O - C - N ANGL. DEV. = -13.5 DEGREES REMARK 500 PRO B 254 C - N - CD ANGL. DEV. = -16.1 DEGREES REMARK 500 PRO A 252 O - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 PRO A 254 C - N - CA ANGL. DEV. = 11.8 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 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 ASN B 54 9.80 58.09 REMARK 500 ALA B 69 -141.52 57.21 REMARK 500 VAL B 103 -135.82 -124.26 REMARK 500 GLU B 163 -35.76 -142.86 REMARK 500 GLU B 196 -131.10 -108.68 REMARK 500 LEU B 220 -115.54 -115.28 REMARK 500 ASN A 54 14.24 59.35 REMARK 500 ALA A 69 -139.30 53.39 REMARK 500 VAL A 103 -135.68 -128.13 REMARK 500 ASN A 106 45.05 -140.58 REMARK 500 GLU A 163 -38.93 -131.55 REMARK 500 GLU A 196 -138.27 -108.47 REMARK 500 LEU A 220 -117.27 -112.29 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 VAL B 57 -10.90 REMARK 500 PRO B 252 23.33 REMARK 500 PRO A 252 19.96 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 Di-peptide CED A 301 and SER A REMARK 800 70 DBREF 5ZG6 B 26 295 UNP P00808 BLAC_BACLI 43 307 DBREF 5ZG6 A 26 295 UNP P00808 BLAC_BACLI 43 307 SEQADV 5ZG6 GLY B 23 UNP P00808 EXPRESSION TAG SEQADV 5ZG6 PRO B 24 UNP P00808 EXPRESSION TAG SEQADV 5ZG6 MET B 25 UNP P00808 EXPRESSION TAG SEQADV 5ZG6 TYR B 166 UNP P00808 GLU 180 ENGINEERED MUTATION SEQADV 5ZG6 GLY A 23 UNP P00808 EXPRESSION TAG SEQADV 5ZG6 PRO A 24 UNP P00808 EXPRESSION TAG SEQADV 5ZG6 MET A 25 UNP P00808 EXPRESSION TAG SEQADV 5ZG6 TYR 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 TYR 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 TYR 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 *106(H2 O) HELIX 1 AA1 ASP B 31 ASP B 41 1 11 HELIX 2 AA2 THR B 71 LYS B 86 1 14 HELIX 3 AA3 ILE B 88 ASN B 92 5 5 HELIX 4 AA4 THR B 98 LEU B 102 5 5 HELIX 5 AA5 ILE B 108 HIS B 112 5 5 HELIX 6 AA6 LEU B 119 SER B 130 1 12 HELIX 7 AA7 ASP B 131 GLY B 143 1 13 HELIX 8 AA8 GLY B 143 GLY B 156 1 14 HELIX 9 AA9 PRO B 167 GLU B 171 5 5 HELIX 10 AB1 THR B 182 LEU B 195 1 14 HELIX 11 AB2 PRO B 200 ARG B 213 1 14 HELIX 12 AB3 LEU B 220 VAL B 225 5 6 HELIX 13 AB4 ASP B 275 ASN B 291 1 17 HELIX 14 AB5 ASP A 32 ASP A 41 1 10 HELIX 15 AB6 THR A 71 LYS A 86 1 14 HELIX 16 AB7 ILE A 88 ASN A 92 5 5 HELIX 17 AB8 THR A 98 LEU A 102 5 5 HELIX 18 AB9 ILE A 108 HIS A 112 5 5 HELIX 19 AC1 LEU A 119 SER A 130 1 12 HELIX 20 AC2 ASP A 131 ILE A 142 1 12 HELIX 21 AC3 GLY A 144 ILE A 155 1 12 HELIX 22 AC4 PRO A 167 GLU A 171 5 5 HELIX 23 AC5 THR A 182 GLU A 196 1 15 HELIX 24 AC6 PRO A 200 ARG A 213 1 14 HELIX 25 AC7 LEU A 220 VAL A 225 5 6 HELIX 26 AC8 ASP A 276 ASN A 291 1 16 SHEET 1 AA1 5 THR B 56 TYR B 60 0 SHEET 2 AA1 5 LYS B 43 ASP B 50 -1 N ILE B 46 O TYR B 60 SHEET 3 AA1 5 VAL B 259 SER B 266 -1 O LEU B 264 N GLY B 45 SHEET 4 AA1 5 THR B 243 TRP B 251 -1 N ILE B 250 O VAL B 259 SHEET 5 AA1 5 GLU B 230 ALA B 238 -1 N GLU B 230 O TRP B 251 SHEET 1 AA2 2 PHE B 66 ALA B 67 0 SHEET 2 AA2 2 THR B 180 SER B 181 -1 O SER B 181 N PHE B 66 SHEET 1 AA3 2 ARG B 94 ILE B 95 0 SHEET 2 AA3 2 MET B 117 THR B 118 -1 O MET B 117 N ILE B 95 SHEET 1 AA4 5 THR A 56 TYR A 60 0 SHEET 2 AA4 5 LYS A 43 ASP A 50 -1 N ILE A 46 O TYR A 60 SHEET 3 AA4 5 VAL A 259 SER A 266 -1 O LEU A 264 N GLY A 45 SHEET 4 AA4 5 THR A 243 TRP A 251 -1 N ILE A 250 O VAL A 259 SHEET 5 AA4 5 GLU A 230 ALA A 238 -1 N LYS A 234 O ILE A 247 SHEET 1 AA5 2 PHE A 66 ALA A 67 0 SHEET 2 AA5 2 THR A 180 SER A 181 -1 O SER A 181 N PHE A 66 SHEET 1 AA6 2 ARG A 94 ILE A 95 0 SHEET 2 AA6 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 1.37 LINK OG SER A 70 C8 CED A 301 1555 1555 1.37 CISPEP 1 TYR B 166 PRO B 167 0 2.46 CISPEP 2 TYR A 166 PRO A 167 0 -4.67 SITE 1 AC1 13 ASP A 114 ALA B 69 SER B 70 TYR B 105 SITE 2 AC1 13 SER B 130 ASN B 132 TYR B 166 ASN B 170 SITE 3 AC1 13 LYS B 234 THR B 235 GLY B 236 ALA B 237 SITE 4 AC1 13 ARG B 244 SITE 1 AC2 17 PHE A 68 ALA A 69 THR A 71 ILE A 72 SITE 2 AC2 17 LYS A 73 TYR A 105 SER A 130 ASN A 132 SITE 3 AC2 17 TYR A 166 ASN A 170 LYS A 234 THR A 235 SITE 4 AC2 17 GLY A 236 ALA A 237 ARG A 244 HOH A 401 SITE 5 AC2 17 ASP B 114 CRYST1 43.292 46.459 65.981 77.43 75.53 69.34 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 0.023099 -0.008709 -0.004764 0.00000 SCALE2 0.000000 0.023004 -0.003322 0.00000 SCALE3 0.000000 0.000000 0.015815 0.00000