HEADER HYDROLASE 10-JUL-16 5GL9 TITLE CRYSTAL STRUCTURE OF THE CLASS A BETA-LACTAMASE PENL COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-294; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA THAILANDENSIS; SOURCE 3 ORGANISM_TAXID: 57975; SOURCE 4 GENE: A8H35_31635; 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: PET28A(+) KEYWDS PENL, OMEGA LOOP, BURKHOLDERIA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.CHOI,H.YI,H.S.KIM,S.H.LEE REVDAT 3 08-NOV-23 5GL9 1 REMARK REVDAT 2 19-FEB-20 5GL9 1 SOURCE DBREF SEQADV REVDAT 1 15-FEB-17 5GL9 0 JRNL AUTH H.YI,J.M.CHOI,J.HWANG,F.PRATI,T.P.CAO,S.H.LEE,H.S.KIM JRNL TITL HIGH ADAPTABILITY OF THE OMEGA LOOP UNDERLIES THE JRNL TITL 2 SUBSTRATE-SPECTRUM-EXTENSION EVOLUTION OF A CLASS A JRNL TITL 3 BETA-LACTAMASE, PENL JRNL REF SCI REP V. 6 36527 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27827433 JRNL DOI 10.1038/SREP36527 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 37006 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1853 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 27.8048 - 3.5256 0.96 2802 155 0.1653 0.1825 REMARK 3 2 3.5256 - 2.7992 1.00 2765 161 0.1665 0.1842 REMARK 3 3 2.7992 - 2.4456 1.00 2748 160 0.1730 0.2079 REMARK 3 4 2.4456 - 2.2221 1.00 2761 129 0.1638 0.1979 REMARK 3 5 2.2221 - 2.0629 1.00 2714 143 0.1555 0.1843 REMARK 3 6 2.0629 - 1.9413 0.99 2699 142 0.1596 0.1799 REMARK 3 7 1.9413 - 1.8441 0.99 2718 131 0.1586 0.1883 REMARK 3 8 1.8441 - 1.7638 0.99 2655 148 0.1673 0.1958 REMARK 3 9 1.7638 - 1.6960 0.99 2697 130 0.1654 0.2067 REMARK 3 10 1.6960 - 1.6374 0.98 2655 140 0.1572 0.2038 REMARK 3 11 1.6374 - 1.5862 0.98 2657 130 0.1535 0.1943 REMARK 3 12 1.5862 - 1.5409 0.99 2640 145 0.1557 0.1831 REMARK 3 13 1.5409 - 1.5003 0.97 2642 139 0.1601 0.1825 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.230 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 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 : 0.006 2053 REMARK 3 ANGLE : 1.057 2782 REMARK 3 CHIRALITY : 0.073 319 REMARK 3 PLANARITY : 0.004 368 REMARK 3 DIHEDRAL : 12.024 748 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 5GL9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300001018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DCM SI(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37054 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 14.40 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 14.50 REMARK 200 R MERGE FOR SHELL (I) : 0.12500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 35.68 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1YLJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.5, 0.1M LI-SULFATE, REMARK 280 30%(W/V) PEG 4000, 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 37.96650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.81850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.96650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.81850 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 TOTAL BURIED SURFACE AREA: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 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 NH1 ARG A 230 NH1 ARG A 270 4444 2.18 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 CYS A 69 -139.99 48.01 REMARK 500 ASP A 87 77.52 -164.17 REMARK 500 TYR A 105 62.10 65.48 REMARK 500 ARG A 220 -118.76 -109.71 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 GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GLD RELATED DB: PDB REMARK 900 RELATED ID: 5GLC RELATED DB: PDB REMARK 900 RELATED ID: 5GLB RELATED DB: PDB REMARK 900 RELATED ID: 5GLA RELATED DB: PDB DBREF1 5GL9 A 26 291 UNP A0A2Z4SUB5_BURTH DBREF2 5GL9 A A0A2Z4SUB5 31 294 SEQADV 5GL9 GLY A 22 UNP A0A2Z4SUB EXPRESSION TAG SEQADV 5GL9 SER A 23 UNP A0A2Z4SUB EXPRESSION TAG SEQADV 5GL9 HIS A 24 UNP A0A2Z4SUB EXPRESSION TAG SEQADV 5GL9 MET A 25 UNP A0A2Z4SUB EXPRESSION TAG SEQRES 1 A 268 GLY SER HIS MET ARG ASN VAL ALA ALA GLU GLN GLN LEU SEQRES 2 A 268 ARG GLU LEU GLU SER THR PHE ASP GLY ARG LEU GLY PHE SEQRES 3 A 268 VAL ALA LEU ASP THR ALA THR GLY ALA ARG ILE ALA HIS SEQRES 4 A 268 ARG ALA ASP GLU ARG PHE PRO PHE CYS SER THR PHE LYS SEQRES 5 A 268 THR MET LEU SER ALA ALA VAL LEU ALA ARG SER ALA GLY SEQRES 6 A 268 ASP ALA ALA LEU LEU GLN ARG ARG ILE PRO TYR ALA LYS SEQRES 7 A 268 ARG ASP LEU VAL ARG TYR SER PRO ILE THR GLU LYS HIS SEQRES 8 A 268 VAL GLY ALA GLY MET THR VAL ALA GLU LEU CYS ALA ALA SEQRES 9 A 268 THR LEU GLN TYR SER ASP ASN THR ALA ALA ASN LEU LEU SEQRES 10 A 268 ILE ALA LEU LEU GLY GLY PRO GLN ALA VAL THR ALA TYR SEQRES 11 A 268 ALA ARG SER ILE GLY ASP ALA THR PHE ARG LEU ASP ARG SEQRES 12 A 268 ARG GLU THR GLU LEU ASN THR ALA ILE PRO GLY ASP GLU SEQRES 13 A 268 ARG ASP THR THR THR PRO ALA ALA MET ALA ALA SER VAL SEQRES 14 A 268 ARG ARG LEU LEU VAL GLY ASP ALA LEU GLY THR ALA GLN SEQRES 15 A 268 ARG ALA GLN LEU ASN ALA TRP MET LEU GLY ASN LYS THR SEQRES 16 A 268 GLY ASP ALA ARG ILE ARG ALA GLY VAL PRO ALA GLY TRP SEQRES 17 A 268 ARG VAL ALA ASP LYS THR GLY THR GLY ASP TYR GLY THR SEQRES 18 A 268 GLY ASN ASP ILE GLY VAL ALA TYR PRO PRO ASP ARG ALA SEQRES 19 A 268 PRO ILE VAL PHE VAL VAL TYR THR THR MET ARG SER ARG SEQRES 20 A 268 ASN ALA GLN ALA ARG ASP ASP VAL ILE ALA SER ALA ALA SEQRES 21 A 268 ARG ILE ALA ALA ARG ALA PHE VAL HET GOL A 301 6 HET GOL A 302 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *336(H2 O) HELIX 1 AA1 SER A 23 SER A 39 1 17 HELIX 2 AA2 THR A 71 ALA A 85 1 15 HELIX 3 AA3 GLY A 86 GLN A 92 5 7 HELIX 4 AA4 ALA A 98 LEU A 102 5 5 HELIX 5 AA5 ILE A 108 VAL A 113 5 6 HELIX 6 AA6 VAL A 119 TYR A 129 1 11 HELIX 7 AA7 ASP A 131 GLY A 143 1 13 HELIX 8 AA8 GLY A 144 ILE A 155 1 12 HELIX 9 AA9 THR A 167 THR A 171 5 5 HELIX 10 AB1 THR A 182 VAL A 195 1 14 HELIX 11 AB2 GLY A 200 GLY A 213 1 14 HELIX 12 AB3 ARG A 220 VAL A 225 1 6 HELIX 13 AB4 ARG A 275 PHE A 290 1 16 SHEET 1 AA1 5 ARG A 57 HIS A 60 0 SHEET 2 AA1 5 GLY A 43 ASP A 51 -1 N PHE A 47 O HIS A 60 SHEET 3 AA1 5 ILE A 259 MET A 267 -1 O TYR A 264 N GLY A 46 SHEET 4 AA1 5 THR A 243 TYR A 251 -1 N ALA A 250 O ILE A 259 SHEET 5 AA1 5 ARG A 230 GLY A 238 -1 N GLY A 236 O ASN A 245 SHEET 1 AA2 2 PHE A 66 PRO A 67 0 SHEET 2 AA2 2 THR A 180 THR A 181 -1 O THR A 181 N PHE A 66 SHEET 1 AA3 2 ARG A 94 TYR A 97 0 SHEET 2 AA3 2 GLY A 114 THR A 118 -1 O GLY A 114 N TYR A 97 CISPEP 1 GLU A 166 THR A 167 0 4.55 SITE 1 AC1 9 GLY A 228 ARG A 230 TYR A 251 PRO A 252 SITE 2 AC1 9 PRO A 254 ARG A 270 ASN A 271 HOH A 402 SITE 3 AC1 9 HOH A 496 SITE 1 AC2 4 ASP A 197 ARG A 284 HOH A 425 HOH A 501 CRYST1 75.933 81.637 36.834 90.00 90.00 90.00 P 21 21 2 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 0.013170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027149 0.00000