HEADER HYDROLASE 19-JAN-05 1YLP TITLE ATOMIC RESOLUTION STRUCTURE OF CTX-M-27 BETA-LACTAMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE CTX-M-27; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CTX-M; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-9A KEYWDS CTX-M, BETA-LACTAMASE, ANISOTROPY, EXTENDED-SPECTRUM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,J.DELMAS,J.SIROT,B.SHOICHET,R.BONNET REVDAT 4 23-AUG-23 1YLP 1 HETSYN REVDAT 3 29-JUL-20 1YLP 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL LINK SITE ATOM REVDAT 2 24-FEB-09 1YLP 1 VERSN REVDAT 1 19-APR-05 1YLP 0 JRNL AUTH Y.CHEN,J.DELMAS,J.SIROT,B.SHOICHET,R.BONNET JRNL TITL ATOMIC RESOLUTION STRUCTURES OF CTX-M BETA-LACTAMASES: JRNL TITL 2 EXTENDED SPECTRUM ACTIVITIES FROM INCREASED MOBILITY AND JRNL TITL 3 DECREASED STABILITY. JRNL REF J.MOL.BIOL. V. 348 349 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15811373 JRNL DOI 10.1016/J.JMB.2005.02.010 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.132 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.132 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 3.400 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2189 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 65174 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.123 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.124 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 3.800 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2118 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 56130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1964 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2295.3 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1892.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 30 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 22177 REMARK 3 NUMBER OF RESTRAINTS : 30067 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.140 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.042 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.015 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.026 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.060 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ANISOTROPIC REFINEMENT. RIDING HYDROGENS INCLUDED IN REMARK 3 REFINEMENT. WATER MOLECULES IN CLOSE CONTACT HAVE A REMARK 3 COMBINED OCCUPANCY OF 1 REMARK 4 REMARK 4 1YLP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11587 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69072 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 22.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 16.40 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 1YLJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM ACETATE, PH REMARK 280 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 4.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 20.76850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.99650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.39200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.99650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.76850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.39200 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: 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 TYR A 264 CB - CG - CD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 TYR A 264 CG - CD1 - CE1 ANGL. DEV. = 5.3 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 THR A 26 119.31 -20.11 REMARK 500 CYS A 69 -134.83 46.01 REMARK 500 VAL A 103 -134.09 -115.36 REMARK 500 SER A 220 -128.58 -103.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LYP RELATED DB: PDB REMARK 900 RELATED ID: 1YLJ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS SEQUENCE DIFFERS FROM THE CANONICAL CTX-M-27 SEQUENCE REMARK 999 BY A SPONTANEOUS MUTATION, P99H. DBREF 1YLP A 25 290 UNP Q840M4 Q840M4_ECOLI 29 291 SEQADV 1YLP HIS A 99 UNP Q840M4 PRO 102 SEE REMARK 999 SEQRES 1 A 263 GLN THR SER ALA VAL GLN GLN LYS LEU ALA ALA LEU GLU SEQRES 2 A 263 LYS SER SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASP SEQRES 3 A 263 THR ALA ASP ASN THR GLN VAL LEU TYR ARG GLY ASP GLU SEQRES 4 A 263 ARG PHE PRO MET CYS SER THR SER LYS VAL MET ALA ALA SEQRES 5 A 263 ALA ALA VAL LEU LYS GLN SER GLU THR GLN LYS GLN LEU SEQRES 6 A 263 LEU ASN GLN PRO VAL GLU ILE LYS HIS ALA ASP LEU VAL SEQRES 7 A 263 ASN TYR ASN PRO ILE ALA GLU LYS HIS VAL ASN GLY THR SEQRES 8 A 263 MET THR LEU ALA GLU LEU SER ALA ALA ALA LEU GLN TYR SEQRES 9 A 263 SER ASP ASN THR ALA MET ASN LYS LEU ILE ALA GLN LEU SEQRES 10 A 263 GLY GLY PRO GLY GLY VAL THR ALA PHE ALA ARG ALA ILE SEQRES 11 A 263 GLY ASP GLU THR PHE ARG LEU ASP ARG THR GLU PRO THR SEQRES 12 A 263 LEU ASN THR ALA ILE PRO GLY ASP PRO ARG ASP THR THR SEQRES 13 A 263 THR PRO ARG ALA MET ALA GLN THR LEU ARG GLN LEU THR SEQRES 14 A 263 LEU GLY HIS ALA LEU GLY GLU THR GLN ARG ALA GLN LEU SEQRES 15 A 263 VAL THR TRP LEU LYS GLY ASN THR THR GLY ALA ALA SER SEQRES 16 A 263 ILE ARG ALA GLY LEU PRO THR SER TRP THR VAL GLY ASP SEQRES 17 A 263 LYS THR GLY SER GLY GLY TYR GLY THR THR ASN ASP ILE SEQRES 18 A 263 ALA VAL ILE TRP PRO GLN GLY ARG ALA PRO LEU VAL LEU SEQRES 19 A 263 VAL THR TYR PHE THR GLN PRO GLN GLN ASN ALA GLU SER SEQRES 20 A 263 ARG ARG ASP VAL LEU ALA SER ALA ALA ARG ILE ILE ALA SEQRES 21 A 263 GLU GLY LEU HET GLC B 1 11 HET FRU B 2 12 HET SO4 A1001 10 HET SO4 A1002 5 HET SO4 A1003 5 HET SO4 A1004 5 HET SO4 A1005 5 HET SO4 A1007 5 HET SO4 A1008 5 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM SO4 SULFATE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE FORMUL 2 GLC C6 H12 O6 FORMUL 2 FRU C6 H12 O6 FORMUL 3 SO4 7(O4 S 2-) FORMUL 10 HOH *320(H2 O) HELIX 1 1 SER A 27 GLY A 41 1 15 HELIX 2 2 CYS A 69 THR A 71 5 3 HELIX 3 3 SER A 72 GLU A 85 1 14 HELIX 4 4 GLN A 89 ASN A 92 5 4 HELIX 5 5 LYS A 98 LEU A 102 5 5 HELIX 6 6 ILE A 108 VAL A 113 5 6 HELIX 7 7 LEU A 119 SER A 130 1 12 HELIX 8 8 ASP A 131 LEU A 142 1 12 HELIX 9 9 GLY A 144 ILE A 155 1 12 HELIX 10 10 PRO A 167 THR A 171 5 5 HELIX 11 11 THR A 182 LEU A 195 1 14 HELIX 12 12 GLY A 200 GLY A 213 1 14 HELIX 13 13 SER A 220 LEU A 225 5 6 HELIX 14 14 ARG A 275 GLY A 289 1 15 SHEET 1 A 5 THR A 55 TYR A 60 0 SHEET 2 A 5 ARG A 43 ASP A 50 -1 N VAL A 46 O TYR A 60 SHEET 3 A 5 LEU A 259 THR A 266 -1 O TYR A 264 N GLY A 45 SHEET 4 A 5 THR A 243 TRP A 251 -1 N ILE A 250 O LEU A 259 SHEET 5 A 5 THR A 230 GLY A 238 -1 N THR A 230 O TRP A 251 SHEET 1 B 2 PHE A 66 PRO A 67 0 SHEET 2 B 2 THR A 180 THR A 181 -1 O THR A 181 N PHE A 66 SHEET 1 C 2 PRO A 94 ILE A 97 0 SHEET 2 C 2 GLY A 115 THR A 118 -1 O MET A 117 N VAL A 95 LINK C1 GLC B 1 O2 FRU B 2 1555 1555 1.44 CISPEP 1 GLU A 166 PRO A 167 0 2.36 CRYST1 41.537 62.784 85.993 90.00 90.00 90.00 P 21 21 21 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 0.024075 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011629 0.00000