HEADER HYDROLASE 10-JUL-16 5GLB TITLE CRYSTAL STRUCTURE OF THE CLASS A BETA-LACTAMASE PENL-TTR10 IN COMPLEX TITLE 2 WITH CBA 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-TTR10, OMEGA LOOP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.CHOI,H.YI,H.S.KIM,S.H.LEE REVDAT 3 08-NOV-23 5GLB 1 REMARK REVDAT 2 19-FEB-20 5GLB 1 SOURCE REMARK DBREF SEQADV REVDAT 2 2 1 LINK REVDAT 1 15-FEB-17 5GLB 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1561 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 32.7828 - 3.5565 1.00 2849 152 0.1621 0.1828 REMARK 3 2 3.5565 - 2.8234 1.00 2742 139 0.1703 0.2132 REMARK 3 3 2.8234 - 2.4666 1.00 2669 159 0.1690 0.2011 REMARK 3 4 2.4666 - 2.2412 1.00 2651 154 0.1573 0.1840 REMARK 3 5 2.2412 - 2.0805 1.00 2707 104 0.1493 0.1918 REMARK 3 6 2.0805 - 1.9579 1.00 2615 152 0.1527 0.1875 REMARK 3 7 1.9579 - 1.8599 1.00 2651 150 0.1498 0.2079 REMARK 3 8 1.8599 - 1.7789 1.00 2643 127 0.1625 0.2119 REMARK 3 9 1.7789 - 1.7104 1.00 2601 163 0.1697 0.2465 REMARK 3 10 1.7104 - 1.6514 1.00 2648 127 0.1643 0.2174 REMARK 3 11 1.6514 - 1.5998 1.00 2595 134 0.1613 0.2235 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.080 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 : 0.007 2064 REMARK 3 ANGLE : 1.213 2799 REMARK 3 CHIRALITY : 0.071 319 REMARK 3 PLANARITY : 0.004 369 REMARK 3 DIHEDRAL : 15.506 766 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 5GLB 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_1300001020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30982 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 0.31500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.714 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: 5GL9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEGMME 2000, 0.1M K-THIOCYANATE, REMARK 280 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 35.02950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.44050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.02950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.44050 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 174 REMARK 465 GLY A 175 REMARK 465 ASP A 176 REMARK 465 GLU A 177 REMARK 465 ARG A 178 REMARK 465 ASP A 179 REMARK 465 THR A 180 REMARK 465 THR A 181 REMARK 465 THR A 182 REMARK 465 ILE A 183 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 OG SER A 70 B CB4 A 401 1.65 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 -139.52 47.22 REMARK 500 TYR A 105 79.90 68.74 REMARK 500 ARG A 230 -120.84 -111.88 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 CB4 A 401 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: 5GLA RELATED DB: PDB REMARK 900 RELATED ID: 5GL9 RELATED DB: PDB DBREF1 5GLB A 26 301 UNP A0A2Z4SUB5_BURTH DBREF2 5GLB A A0A2Z4SUB5 31 294 SEQADV 5GLB GLY A 22 UNP A0A2Z4SUB EXPRESSION TAG SEQADV 5GLB SER A 23 UNP A0A2Z4SUB EXPRESSION TAG SEQADV 5GLB HIS A 24 UNP A0A2Z4SUB EXPRESSION TAG SEQADV 5GLB MET A 25 UNP A0A2Z4SUB EXPRESSION TAG SEQADV 5GLB ILE A 173 UNP A0A2Z4SUB INSERTION SEQADV 5GLB PRO A 174 UNP A0A2Z4SUB INSERTION SEQADV 5GLB GLY A 175 UNP A0A2Z4SUB INSERTION SEQADV 5GLB ASP A 176 UNP A0A2Z4SUB INSERTION SEQADV 5GLB GLU A 177 UNP A0A2Z4SUB INSERTION SEQADV 5GLB ARG A 178 UNP A0A2Z4SUB INSERTION SEQADV 5GLB ASP A 179 UNP A0A2Z4SUB INSERTION SEQADV 5GLB THR A 180 UNP A0A2Z4SUB INSERTION SEQADV 5GLB THR A 181 UNP A0A2Z4SUB INSERTION SEQADV 5GLB THR A 182 UNP A0A2Z4SUB INSERTION SEQRES 1 A 278 GLY SER HIS MET ARG ASN VAL ALA ALA GLU GLN GLN LEU SEQRES 2 A 278 ARG GLU LEU GLU SER THR PHE ASP GLY ARG LEU GLY PHE SEQRES 3 A 278 VAL ALA LEU ASP THR ALA THR GLY ALA ARG ILE ALA HIS SEQRES 4 A 278 ARG ALA ASP GLU ARG PHE PRO PHE CYS SER THR PHE LYS SEQRES 5 A 278 THR MET LEU SER ALA ALA VAL LEU ALA ARG SER ALA GLY SEQRES 6 A 278 ASP ALA ALA LEU LEU GLN ARG ARG ILE PRO TYR ALA LYS SEQRES 7 A 278 ARG ASP LEU VAL ARG TYR SER PRO ILE THR GLU LYS HIS SEQRES 8 A 278 VAL GLY ALA GLY MET THR VAL ALA GLU LEU CYS ALA ALA SEQRES 9 A 278 THR LEU GLN TYR SER ASP ASN THR ALA ALA ASN LEU LEU SEQRES 10 A 278 ILE ALA LEU LEU GLY GLY PRO GLN ALA VAL THR ALA TYR SEQRES 11 A 278 ALA ARG SER ILE GLY ASP ALA THR PHE ARG LEU ASP ARG SEQRES 12 A 278 ARG GLU THR GLU LEU ASN THR ALA ILE PRO GLY ASP GLU SEQRES 13 A 278 ARG ASP THR THR THR ILE PRO GLY ASP GLU ARG ASP THR SEQRES 14 A 278 THR THR PRO ALA ALA MET ALA ALA SER VAL ARG ARG LEU SEQRES 15 A 278 LEU VAL GLY ASP ALA LEU GLY THR ALA GLN ARG ALA GLN SEQRES 16 A 278 LEU ASN ALA TRP MET LEU GLY ASN LYS THR GLY ASP ALA SEQRES 17 A 278 ARG ILE ARG ALA GLY VAL PRO ALA GLY TRP ARG VAL ALA SEQRES 18 A 278 ASP LYS THR GLY THR GLY ASP TYR GLY THR GLY ASN ASP SEQRES 19 A 278 ILE GLY VAL ALA TYR PRO PRO ASP ARG ALA PRO ILE VAL SEQRES 20 A 278 PHE VAL VAL TYR THR THR MET ARG SER ARG ASN ALA GLN SEQRES 21 A 278 ALA ARG ASP ASP VAL ILE ALA SER ALA ALA ARG ILE ALA SEQRES 22 A 278 ALA ARG ALA PHE VAL HET CB4 A 401 22 HETNAM CB4 PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)- HETNAM 2 CB4 4-THIAZOLEACETYL]AMINO]METHANEBORONATE FORMUL 2 CB4 C10 H15 B N4 O6 S FORMUL 3 HOH *255(H2 O) HELIX 1 AA1 SER A 23 THR A 40 1 18 HELIX 2 AA2 THR A 71 ALA A 85 1 15 HELIX 3 AA3 ALA A 89 GLN A 92 5 4 HELIX 4 AA4 ALA A 98 LEU A 102 5 5 HELIX 5 AA5 ILE A 108 HIS A 112 5 5 HELIX 6 AA6 VAL A 119 SER A 130 1 12 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 192 VAL A 205 1 14 HELIX 11 AB2 GLY A 210 GLY A 223 1 14 HELIX 12 AB3 ARG A 230 VAL A 235 5 6 HELIX 13 AB4 ARG A 285 VAL A 301 1 17 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 269 MET A 277 -1 O TYR A 274 N GLY A 46 SHEET 4 AA1 5 THR A 253 TYR A 261 -1 N ALA A 260 O ILE A 269 SHEET 5 AA1 5 ARG A 240 GLY A 248 -1 N GLY A 246 O ASN A 255 SHEET 1 AA2 2 PHE A 66 PRO A 67 0 SHEET 2 AA2 2 THR A 190 THR A 191 -1 O THR A 191 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 1.59 SITE 1 AC1 15 CYS A 69 SER A 70 TYR A 105 TYR A 129 SITE 2 AC1 15 SER A 130 ASN A 132 ASN A 170 ASP A 207 SITE 3 AC1 15 LEU A 209 THR A 226 GLY A 246 THR A 247 SITE 4 AC1 15 HOH A 505 HOH A 506 HOH A 543 CRYST1 70.059 92.881 34.993 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 0.014274 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028577 0.00000