HEADER HYDROLASE 09-FEB-05 1YT4 TITLE CRYSTAL STRUCTURE OF TEM-76 BETA-LACTAMASE AT 1.4 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE TEM; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TEM; COMPND 5 SYNONYM: TEM-1, TEM-2, TEM-3, TEM-4, TEM-5, TEM-6, TEM-8/CAZ-2, TEM- COMPND 6 16/CAZ-7, TEM-24/CAZ-6, IRT-4, PENICILLINASE; COMPND 7 EC: 3.5.2.6; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BLA; 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: PET24A(+) KEYWDS TEM-1, BETA-LACTAMASE, INHIBITOR RESISTANCE, IRT, S130G, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.L.THOMAS,D.GOLEMI-KOTRA,C.KIM,S.B.VAKULENKO,S.MOBASHERY, AUTHOR 2 B.K.SHOICHET REVDAT 5 09-OCT-24 1YT4 1 REMARK REVDAT 4 23-AUG-23 1YT4 1 REMARK REVDAT 3 20-OCT-21 1YT4 1 SEQADV REVDAT 2 24-FEB-09 1YT4 1 VERSN REVDAT 1 12-JUL-05 1YT4 0 JRNL AUTH V.L.THOMAS,D.GOLEMI-KOTRA,C.KIM,S.B.VAKULENKO,S.MOBASHERY, JRNL AUTH 2 B.K.SHOICHET JRNL TITL STRUCTURAL CONSEQUENCES OF THE INHIBITOR-RESISTANT SER130GLY JRNL TITL 2 SUBSTITUTION IN TEM BETA-LACTAMASE. JRNL REF BIOCHEMISTRY V. 44 9330 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15981999 JRNL DOI 10.1021/BI0502700 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 42512 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) : 0.183 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2126 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2025 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 326 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.570 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 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) : 1.03321 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL 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 : 43334 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 8.150 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.370 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1JWP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM POTASSIUM PHOSPHATE, PH 8.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K 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 20.80050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.18000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.85350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.18000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.80050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.85350 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: 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 O GLU A 166 CA PRO A 167 1.67 REMARK 500 C GLU A 166 CA PRO A 167 1.73 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 GLU A 166 N - CA - C ANGL. DEV. = 21.6 DEGREES REMARK 500 PRO A 167 C - N - CA ANGL. DEV. = -44.2 DEGREES REMARK 500 PRO A 167 C - N - CD ANGL. DEV. = 25.1 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 MET A 69 -147.16 55.04 REMARK 500 TYR A 105 81.48 62.43 REMARK 500 TYR A 105 82.91 59.86 REMARK 500 ASN A 175 -0.30 71.53 REMARK 500 LEU A 220 -122.75 -96.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JWP RELATED DB: PDB REMARK 900 RELATED ID: 1LI0 RELATED DB: PDB REMARK 900 RELATED ID: 1TDL RELATED DB: PDB DBREF 1YT4 A 26 288 UNP P62593 BLAT_ECOLI 24 286 SEQADV 1YT4 GLY A 130 UNP P62593 SER 128 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 VAL 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 GLY 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 ALA 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 FORMUL 2 HOH *326(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 MET A 129 1 11 HELIX 6 6 ASP A 131 GLY A 143 1 13 HELIX 7 7 GLY A 143 MET A 155 1 13 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 GLU A 48 O LEU A 57 SHEET 3 A 5 ARG A 259 THR A 266 -1 O TYR A 264 N GLY A 45 SHEET 4 A 5 ARG A 244 GLY A 251 -1 N ILE A 246 O ILE A 263 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 2.34 CRYST1 41.601 59.707 88.360 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 0.024038 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011317 0.00000