HEADER HYDROLASE 27-APR-99 1CK3 TITLE N276D MUTANT OF ESCHERICHIA COLI TEM-1 BETA-LACTAMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: MV1190; SOURCE 7 EXPRESSION_SYSTEM_CELLULAR_LOCATION: PERIPLASM; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTZ18U KEYWDS BETA-LACTAMASE, CLAVULANATE-RESISTANT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.SWAREN,L.MAVEYRAUD,J.P.SAMAMA REVDAT 7 09-AUG-23 1CK3 1 REMARK REVDAT 6 03-NOV-21 1CK3 1 SEQADV REVDAT 5 04-OCT-17 1CK3 1 REMARK REVDAT 4 24-FEB-09 1CK3 1 VERSN REVDAT 3 01-APR-03 1CK3 1 JRNL REVDAT 2 28-JUN-00 1CK3 3 ATOM DBREF REMARK SEQADV REVDAT 2 2 3 SEQRES REVDAT 1 18-AUG-99 1CK3 0 JRNL AUTH P.SWAREN,D.GOLEMI,S.CABANTOUS,A.BULYCHEV,L.MAVEYRAUD, JRNL AUTH 2 S.MOBASHERY,J.P.SAMAMA JRNL TITL X-RAY STRUCTURE OF THE ASN276ASP VARIANT OF THE ESCHERICHIA JRNL TITL 2 COLI TEM-1 BETA-LACTAMASE: DIRECT OBSERVATION OF JRNL TITL 3 ELECTROSTATIC MODULATION IN RESISTANCE TO INACTIVATION BY JRNL TITL 4 CLAVULANIC ACID. JRNL REF BIOCHEMISTRY V. 38 9570 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10423234 JRNL DOI 10.1021/BI990758Z REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1537256.890 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.5 REMARK 3 NUMBER OF REFLECTIONS : 8755 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 SET) : 0.165 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.400 REMARK 3 FREE R VALUE TEST SET COUNT : 563 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1044 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 77 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2001 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : 1.36000 REMARK 3 B33 (A**2) : -1.88000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.090 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.600 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.710 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.200 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.570 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000000956. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : APR-95 REMARK 200 TEMPERATURE (KELVIN) : 277.0 REMARK 200 PH : 7.80 REMARK 200 NUMBER OF CRYSTALS USED : 3 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, ROTAVATA/AGROVATA REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8771 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 24.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.6 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.07700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1BTL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.80 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 20.91000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.32500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.18000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.32500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.91000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.18000 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 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 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 55 CG CD CE NZ REMARK 470 GLN A 99 CG CD OE1 NE2 REMARK 470 LYS A 111 CD CE NZ REMARK 470 LYS A 146 CG CD CE NZ REMARK 470 GLU A 197 CG CD OE1 OE2 REMARK 470 LEU A 198 CG CD1 CD2 REMARK 470 LYS A 215 CD CE NZ REMARK 470 LYS A 256 CG CD CE NZ 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 A 52 -77.94 -68.40 REMARK 500 MET A 69 -142.59 65.10 REMARK 500 TYR A 105 76.34 54.49 REMARK 500 ASN A 175 -2.30 75.31 REMARK 500 LEU A 220 -129.92 -88.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 1CK3 A 26 288 UNP P62593 BLAT_ECOLI 24 286 SEQADV 1CK3 ILE A 84 UNP P62593 VAL 82 ENGINEERED MUTATION SEQADV 1CK3 VAL A 184 UNP P62593 ALA 182 ENGINEERED MUTATION SEQADV 1CK3 ASP A 276 UNP P62593 ASN 272 ENGINEERED MUTATION SEQRES 1 A 263 HIS PRO GLU THR LEU VAL LYS VAL LYS ASP ALA GLU ASP SEQRES 2 A 263 GLN LEU GLY ALA ARG VAL GLY TYR ILE GLU LEU ASP LEU SEQRES 3 A 263 ASN SER GLY LYS ILE LEU GLU SER PHE ARG PRO GLU GLU SEQRES 4 A 263 ARG PHE PRO MET MET SER THR PHE LYS VAL LEU LEU CYS SEQRES 5 A 263 GLY ALA VAL LEU SER ARG ILE ASP ALA GLY GLN GLU GLN SEQRES 6 A 263 LEU GLY ARG ARG ILE HIS TYR SER GLN ASN ASP LEU VAL SEQRES 7 A 263 GLU TYR SER PRO VAL THR GLU LYS HIS LEU THR ASP GLY SEQRES 8 A 263 MET THR VAL ARG GLU LEU CYS SER ALA ALA ILE THR MET SEQRES 9 A 263 SER ASP ASN THR ALA ALA ASN LEU LEU LEU THR THR ILE SEQRES 10 A 263 GLY GLY PRO LYS GLU LEU THR ALA PHE LEU HIS ASN MET SEQRES 11 A 263 GLY ASP HIS VAL THR ARG LEU ASP ARG TRP GLU PRO GLU SEQRES 12 A 263 LEU ASN GLU ALA ILE PRO ASN ASP GLU ARG ASP THR THR SEQRES 13 A 263 MET PRO VAL ALA MET ALA THR THR LEU ARG LYS LEU LEU SEQRES 14 A 263 THR GLY GLU LEU LEU THR LEU ALA SER ARG GLN GLN LEU SEQRES 15 A 263 ILE ASP TRP MET GLU ALA ASP LYS VAL ALA GLY PRO LEU SEQRES 16 A 263 LEU ARG SER ALA LEU PRO ALA GLY TRP PHE ILE ALA ASP SEQRES 17 A 263 LYS SER GLY ALA GLY GLU ARG GLY SER ARG GLY ILE ILE SEQRES 18 A 263 ALA ALA LEU GLY PRO ASP GLY LYS PRO SER ARG ILE VAL SEQRES 19 A 263 VAL ILE TYR THR THR GLY SER GLN ALA THR MET ASP GLU SEQRES 20 A 263 ARG ASP ARG GLN ILE ALA GLU ILE GLY ALA SER LEU ILE SEQRES 21 A 263 LYS HIS TRP FORMUL 2 HOH *76(H2 O) HELIX 1 1 HIS A 26 GLY A 41 1 16 HELIX 2 2 THR A 71 ALA A 86 1 16 HELIX 3 3 SER A 98 LEU A 102 5 5 HELIX 4 4 VAL A 108 HIS A 112 5 5 HELIX 5 5 VAL A 119 THR A 128 1 10 HELIX 6 6 ASP A 131 GLY A 143 1 13 HELIX 7 7 GLY A 143 ASN A 154 1 12 HELIX 8 8 PRO A 167 GLU A 171 5 5 HELIX 9 9 MET A 182 GLY A 196 1 15 HELIX 10 10 THR A 200 ALA A 213 1 14 HELIX 11 11 LEU A 220 LEU A 225 5 6 HELIX 12 12 THR A 271 HIS A 289 1 19 SHEET 1 A 5 ILE A 56 PHE A 60 0 SHEET 2 A 5 ARG A 43 ASP A 50 -1 N TYR A 46 O PHE A 60 SHEET 3 A 5 ARG A 259 THR A 266 -1 O ILE A 260 N LEU A 49 SHEET 4 A 5 ARG A 244 GLY A 251 -1 N ARG A 244 O THR A 265 SHEET 5 A 5 PHE A 230 ALA A 237 -1 N PHE A 230 O GLY 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 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 SSBOND 1 CYS A 77 CYS A 123 1555 1555 2.03 CISPEP 1 GLU A 166 PRO A 167 0 0.02 CRYST1 41.820 60.360 88.650 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 0.023912 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011280 0.00000