HEADER HYDROLASE 14-OCT-97 1AXB TITLE TEM-1 BETA-LACTAMASE FROM ESCHERICHIA COLI INHIBITED WITH TITLE 2 AN ACYLATION TRANSITION STATE ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: TEM-1 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 CELLULAR_LOCATION: PERIPLASM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PBR322 KEYWDS HYDROLASE, ANTIBIOTIC RESISTANCE, BETA-LACTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR L.MAVEYRAUD,R.F.PRATT,J.P.SAMAMA REVDAT 3 24-FEB-09 1AXB 1 VERSN REVDAT 2 18-NOV-98 1AXB 1 COMPND REMARK JRNL REVDAT 1 28-OCT-98 1AXB 0 JRNL AUTH L.MAVEYRAUD,R.F.PRATT,J.P.SAMAMA JRNL TITL CRYSTAL STRUCTURE OF AN ACYLATION TRANSITION-STATE JRNL TITL 2 ANALOG OF THE TEM-1 BETA-LACTAMASE. MECHANISTIC JRNL TITL 3 IMPLICATIONS FOR CLASS A BETA-LACTAMASES. JRNL REF BIOCHEMISTRY V. 37 2622 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9485412 JRNL DOI 10.1021/BI972501B REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 14660 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) : 0.156 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1494 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.58 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1053 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE : 0.2280 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 102 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2030 REMARK 3 NUCLEIC ACID ATOMS : NULL REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.34 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.25 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.20 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.173 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.998 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.077 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.909 ; 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 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A PHOSPHONYLATED SERINE RESIDUE WAS REMARK 3 INTRODUCED IN THE ENGH & HUBER PARAMETER FILE REMARK 4 REMARK 4 1AXB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-95 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 7.8 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : DOUBLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS (MSC) REMARK 200 DATA SCALING SOFTWARE : PROCESS (MSC) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14698 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : NULL 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) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14400 REMARK 200 R SYM FOR SHELL (I) : 0.14400 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER DIFFERENCE REMARK 200 METHOD, STARTING WITH 1BTL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BUFFER NA/K-PHOSPHATE 20MM PH 7.8 REMARK 280 AMMONIUM SULFATE 45% SATURATION (4 DEGREES) ACETONE 4% (V/V) REMARK 280 PROTEIN 14.5 MG/ML 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 21.02000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.45500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.48500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.45500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.02000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.48500 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 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 MET A 69 -144.07 61.35 REMARK 500 TYR A 105 83.11 62.33 REMARK 500 LEU A 220 -131.12 -79.12 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 FOS A 291 DBREF 1AXB A 26 290 UNP P62593 BLAT_ECOLI 24 286 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 ASN ARG GLN ILE ALA GLU ILE GLY ALA SER LEU ILE SEQRES 21 A 263 LYS HIS TRP HET FOS A 291 15 HETNAM FOS [[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE FORMUL 2 FOS C9 H12 N O5 P FORMUL 3 HOH *127(H2 O) HELIX 1 1 PRO A 27 LEU A 40 1 14 HELIX 2 2 MET A 69 ASP A 85 5 17 HELIX 3 3 GLN A 99 ASP A 101 5 3 HELIX 4 4 THR A 109 LYS A 111 5 3 HELIX 5 5 VAL A 119 THR A 128 1 10 HELIX 6 6 ASN A 132 ILE A 142 1 11 HELIX 7 7 PRO A 145 MET A 155 1 11 HELIX 8 8 GLU A 168 ASN A 170 5 3 HELIX 9 9 PRO A 183 THR A 195 1 13 HELIX 10 10 LEU A 201 GLU A 212 1 12 HELIX 11 11 LEU A 221 ALA A 224 5 4 HELIX 12 12 MET A 272 LYS A 288 1 17 SHEET 1 A 5 PHE A 230 ALA A 237 0 SHEET 2 A 5 ARG A 244 GLY A 251 -1 N GLY A 251 O PHE A 230 SHEET 3 A 5 ARG A 259 THR A 266 -1 N THR A 265 O ARG A 244 SHEET 4 A 5 ARG A 43 ASP A 50 -1 N LEU A 49 O ILE A 260 SHEET 5 A 5 ILE A 56 PHE A 60 -1 N PHE A 60 O TYR A 46 SHEET 1 B 2 ARG A 65 PRO A 67 0 SHEET 2 B 2 THR A 180 MET A 182 -1 N THR A 181 O PHE A 66 SSBOND 1 CYS A 77 CYS A 123 1555 1555 2.03 LINK OG SER A 70 P FOS A 291 1555 1555 1.61 CISPEP 1 GLU A 166 PRO A 167 0 0.23 SITE 1 AC1 12 MET A 69 SER A 70 LYS A 111 HIS A 112 SITE 2 AC1 12 ASP A 115 SER A 130 ASN A 132 ASN A 170 SITE 3 AC1 12 GLY A 236 ALA A 237 GLY A 238 GLU A 240 CRYST1 42.040 60.970 88.910 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 0.023787 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011247 0.00000