HEADER HYDROLASE 13-AUG-12 4GKU TITLE CRYSTAL STRUCTURE OF BETA LACTAMASE IN PET-15B COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE TEM; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IRT-4, PENICILLINASE, TEM-1, TEM-16/CAZ-7, TEM-2, TEM- COMPND 5 24/CAZ-6, TEM-3, TEM-4, TEM-5, TEM-6, TEM-8/CAZ-2; COMPND 6 EC: 3.5.2.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BLA, BLAT-3, BLAT-4, BLAT-5, BLAT-6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA LACTAMASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,C.CAO REVDAT 2 13-NOV-24 4GKU 1 REMARK REVDAT 1 10-OCT-12 4GKU 0 JRNL AUTH Y.ZHANG,C.CAO JRNL TITL CRYSTAL STRUCTURE OF BETA LACTAMASE IN PET-15B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 36758 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.790 REMARK 3 FREE R VALUE TEST SET COUNT : 3600 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.9227 - 4.1230 1.00 3428 369 0.1713 0.1975 REMARK 3 2 4.1230 - 3.2733 1.00 3429 370 0.1538 0.1737 REMARK 3 3 3.2733 - 2.8598 0.98 3395 362 0.1728 0.2157 REMARK 3 4 2.8598 - 2.5984 0.98 3346 370 0.1578 0.1988 REMARK 3 5 2.5984 - 2.4122 0.97 3348 393 0.1608 0.1904 REMARK 3 6 2.4122 - 2.2700 0.97 3291 348 0.1549 0.2084 REMARK 3 7 2.2700 - 2.1564 0.97 3336 373 0.1414 0.1646 REMARK 3 8 2.1564 - 2.0625 0.96 3332 351 0.1521 0.2036 REMARK 3 9 2.0625 - 1.9831 0.95 3236 369 0.1696 0.2017 REMARK 3 10 1.9831 - 1.9147 0.87 3017 295 0.2222 0.2914 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 40.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.830 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) : 2.91680 REMARK 3 B22 (A**2) : -1.15810 REMARK 3 B33 (A**2) : -1.75880 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2061 REMARK 3 ANGLE : 1.016 2790 REMARK 3 CHIRALITY : 0.069 321 REMARK 3 PLANARITY : 0.004 363 REMARK 3 DIHEDRAL : 13.739 775 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2605 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37743 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 100.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM CHLORIDE, 0.1M BIS REMARK 280 -TRIS, 25% PEG 3350, PH 6.5, VAPOR DIFFUSION, TEMPERATURE 293K 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 23.50450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.36150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.40850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.36150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.50450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.40850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 HOH A 516 O HOH A 594 2.02 REMARK 500 NE ARG A 238 O HOH A 591 2.08 REMARK 500 O HOH A 437 O HOH A 594 2.19 REMARK 500 O HOH A 434 O HOH A 435 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 523 O HOH A 530 4455 2.06 REMARK 500 OE2 GLU A 108 CE1 HIS A 151 3555 2.10 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 67 -147.32 51.69 REMARK 500 TYR A 103 84.97 53.82 REMARK 500 ASN A 173 -1.27 72.55 REMARK 500 LEU A 218 -122.32 -100.94 REMARK 500 SER A 254 -7.28 -140.29 REMARK 500 REMARK 500 REMARK: NULL DBREF 4GKU A 24 286 UNP P62593 BLAT_ECOLX 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 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 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 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 *315(H2 O) HELIX 1 1 HIS A 24 GLY A 39 1 16 HELIX 2 2 THR A 69 ALA A 84 1 16 HELIX 3 3 SER A 96 LEU A 100 5 5 HELIX 4 4 VAL A 106 HIS A 110 5 5 HELIX 5 5 VAL A 117 MET A 127 1 11 HELIX 6 6 ASP A 129 GLY A 141 1 13 HELIX 7 7 GLY A 142 MET A 153 1 12 HELIX 8 8 PRO A 165 GLU A 169 5 5 HELIX 9 9 MET A 180 GLY A 194 1 15 HELIX 10 10 THR A 198 ALA A 211 1 14 HELIX 11 11 LEU A 218 LEU A 223 5 6 HELIX 12 12 THR A 267 HIS A 285 1 19 SHEET 1 A 5 ILE A 54 PHE A 58 0 SHEET 2 A 5 ARG A 41 ASP A 48 -1 N GLU A 46 O LEU A 55 SHEET 3 A 5 ARG A 255 THR A 262 -1 O TYR A 260 N GLY A 43 SHEET 4 A 5 ARG A 241 GLY A 248 -1 N ILE A 243 O ILE A 259 SHEET 5 A 5 PHE A 228 ALA A 235 -1 N PHE A 228 O GLY A 248 SHEET 1 B 2 PHE A 64 PRO A 65 0 SHEET 2 B 2 THR A 178 THR A 179 -1 O THR A 179 N PHE A 64 SHEET 1 C 2 ARG A 92 ILE A 93 0 SHEET 2 C 2 MET A 115 THR A 116 -1 O MET A 115 N ILE A 93 SSBOND 1 CYS A 75 CYS A 121 1555 1555 2.07 CISPEP 1 GLU A 164 PRO A 165 0 3.40 CRYST1 47.009 72.817 74.723 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 0.021273 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013383 0.00000