HEADER HYDROLASE 20-OCT-18 6ILX TITLE CRYSTAL STRUCTURE OF PETASE W159F MUTANT FROM IDEONELLA SAKAIENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY(ETHYLENE TEREPHTHALATE) HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PETASE,PET-DIGESTING ENZYME; COMPND 5 EC: 3.1.1.101; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: IDEONELLA SAKAIENSIS (STRAIN 201-F6); SOURCE 3 ORGANISM_TAXID: 1547922; SOURCE 4 STRAIN: 201-F6; SOURCE 5 GENE: ISF6_4831; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MUTATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.C.LIU,C.SHI REVDAT 3 09-SEP-20 6ILX 1 TITLE REVDAT 2 10-APR-19 6ILX 1 JRNL REVDAT 1 27-MAR-19 6ILX 0 JRNL AUTH C.LIU,C.SHI,S.ZHU,R.WEI,C.C.YIN JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF POLYETHYLENE JRNL TITL 2 TEREPHTHALATE HYDROLASE FROM IDEONELLA SAKAIENSIS. JRNL REF BIOCHEM. BIOPHYS. RES. V. 508 289 2019 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 30502092 JRNL DOI 10.1016/J.BBRC.2018.11.148 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 37628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1900 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 43.8584 - 3.4942 1.00 2921 156 0.1580 0.1642 REMARK 3 2 3.4942 - 2.7736 1.00 2772 167 0.1923 0.2197 REMARK 3 3 2.7736 - 2.4230 1.00 2743 142 0.1936 0.2106 REMARK 3 4 2.4230 - 2.2015 1.00 2754 141 0.1825 0.1875 REMARK 3 5 2.2015 - 2.0437 1.00 2709 139 0.1659 0.2037 REMARK 3 6 2.0437 - 1.9232 0.98 2730 118 0.1617 0.1893 REMARK 3 7 1.9232 - 1.8269 0.99 2641 169 0.1514 0.1888 REMARK 3 8 1.8269 - 1.7473 0.98 2677 146 0.1477 0.1896 REMARK 3 9 1.7473 - 1.6801 0.99 2664 139 0.1480 0.2069 REMARK 3 10 1.6801 - 1.6221 0.98 2663 147 0.1578 0.2097 REMARK 3 11 1.6221 - 1.5714 0.93 2514 139 0.1556 0.1925 REMARK 3 12 1.5714 - 1.5265 0.83 2227 106 0.1477 0.2076 REMARK 3 13 1.5265 - 1.4863 0.74 1974 110 0.1537 0.2146 REMARK 3 14 1.4863 - 1.4500 0.64 1739 81 0.1485 0.2170 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) : 18.180 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 : 0.008 2001 REMARK 3 ANGLE : 1.032 2726 REMARK 3 CHIRALITY : 0.091 299 REMARK 3 PLANARITY : 0.008 361 REMARK 3 DIHEDRAL : 11.878 712 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 6ILX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1300009431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97776 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37628 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.48500 REMARK 200 R SYM (I) : 1.11400 REMARK 200 FOR THE DATA SET : 3.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, PH 5.5, 3M NACL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 25.54350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.68900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.53850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.68900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.54350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.53850 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 MET A 27 REMARK 465 GLN A 28 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 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 ASN A 73 37.32 -148.82 REMARK 500 THR A 88 -9.00 74.37 REMARK 500 SER A 160 -118.84 59.44 REMARK 500 ALA A 209 79.38 -119.56 REMARK 500 SER A 214 -78.35 -125.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 63 O REMARK 620 2 GLY A 64 O 67.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 302 DBREF1 6ILX A 28 290 UNP PETH_IDESA DBREF2 6ILX A A0A0K8P6T7 28 290 SEQADV 6ILX MET A 27 UNP A0A0K8P6T EXPRESSION TAG SEQADV 6ILX PHE A 159 UNP A0A0K8P6T TRP 159 ENGINEERED MUTATION SEQADV 6ILX HIS A 291 UNP A0A0K8P6T EXPRESSION TAG SEQADV 6ILX HIS A 292 UNP A0A0K8P6T EXPRESSION TAG SEQADV 6ILX HIS A 293 UNP A0A0K8P6T EXPRESSION TAG SEQADV 6ILX HIS A 294 UNP A0A0K8P6T EXPRESSION TAG SEQADV 6ILX HIS A 295 UNP A0A0K8P6T EXPRESSION TAG SEQADV 6ILX HIS A 296 UNP A0A0K8P6T EXPRESSION TAG SEQRES 1 A 270 MET GLN THR ASN PRO TYR ALA ARG GLY PRO ASN PRO THR SEQRES 2 A 270 ALA ALA SER LEU GLU ALA SER ALA GLY PRO PHE THR VAL SEQRES 3 A 270 ARG SER PHE THR VAL SER ARG PRO SER GLY TYR GLY ALA SEQRES 4 A 270 GLY THR VAL TYR TYR PRO THR ASN ALA GLY GLY THR VAL SEQRES 5 A 270 GLY ALA ILE ALA ILE VAL PRO GLY TYR THR ALA ARG GLN SEQRES 6 A 270 SER SER ILE LYS TRP TRP GLY PRO ARG LEU ALA SER HIS SEQRES 7 A 270 GLY PHE VAL VAL ILE THR ILE ASP THR ASN SER THR LEU SEQRES 8 A 270 ASP GLN PRO SER SER ARG SER SER GLN GLN MET ALA ALA SEQRES 9 A 270 LEU ARG GLN VAL ALA SER LEU ASN GLY THR SER SER SER SEQRES 10 A 270 PRO ILE TYR GLY LYS VAL ASP THR ALA ARG MET GLY VAL SEQRES 11 A 270 MET GLY PHE SER MET GLY GLY GLY GLY SER LEU ILE SER SEQRES 12 A 270 ALA ALA ASN ASN PRO SER LEU LYS ALA ALA ALA PRO GLN SEQRES 13 A 270 ALA PRO TRP ASP SER SER THR ASN PHE SER SER VAL THR SEQRES 14 A 270 VAL PRO THR LEU ILE PHE ALA CYS GLU ASN ASP SER ILE SEQRES 15 A 270 ALA PRO VAL ASN SER SER ALA LEU PRO ILE TYR ASP SER SEQRES 16 A 270 MET SER ARG ASN ALA LYS GLN PHE LEU GLU ILE ASN GLY SEQRES 17 A 270 GLY SER HIS SER CYS ALA ASN SER GLY ASN SER ASN GLN SEQRES 18 A 270 ALA LEU ILE GLY LYS LYS GLY VAL ALA TRP MET LYS ARG SEQRES 19 A 270 PHE MET ASP ASN ASP THR ARG TYR SER THR PHE ALA CYS SEQRES 20 A 270 GLU ASN PRO ASN SER THR ARG VAL SER ASP PHE ARG THR SEQRES 21 A 270 ALA ASN CYS SER HIS HIS HIS HIS HIS HIS HET CL A 301 1 HET NA A 302 1 HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 2 CL CL 1- FORMUL 3 NA NA 1+ FORMUL 4 HOH *139(H2 O) HELIX 1 AA1 THR A 39 ALA A 45 1 7 HELIX 2 AA2 ARG A 90 LYS A 95 5 6 HELIX 3 AA3 TRP A 96 SER A 103 1 8 HELIX 4 AA4 GLN A 119 GLY A 139 1 21 HELIX 5 AA5 SER A 160 ASN A 173 1 14 HELIX 6 AA6 SER A 214 MET A 222 1 9 HELIX 7 AA7 ASN A 246 ASP A 263 1 18 HELIX 8 AA8 ASP A 265 ARG A 267 5 3 HELIX 9 AA9 TYR A 268 GLU A 274 1 7 SHEET 1 AA1 6 VAL A 52 THR A 56 0 SHEET 2 AA1 6 ALA A 65 PRO A 71 -1 O VAL A 68 N PHE A 55 SHEET 3 AA1 6 VAL A 107 ASP A 112 -1 O VAL A 108 N TYR A 69 SHEET 4 AA1 6 VAL A 78 VAL A 84 1 N ILE A 81 O ILE A 109 SHEET 5 AA1 6 VAL A 149 GLY A 158 1 O ASP A 150 N VAL A 78 SHEET 6 AA1 6 ALA A 178 ALA A 179 1 O ALA A 178 N VAL A 156 SHEET 1 AA2 3 THR A 198 CYS A 203 0 SHEET 2 AA2 3 LYS A 227 ILE A 232 1 O GLN A 228 N ILE A 200 SHEET 3 AA2 3 VAL A 281 ALA A 287 -1 O ARG A 285 N PHE A 229 SSBOND 1 CYS A 203 CYS A 239 1555 1555 2.04 SSBOND 2 CYS A 273 CYS A 289 1555 1555 2.06 LINK O TYR A 63 NA NA A 302 1555 1555 3.11 LINK O GLY A 64 NA NA A 302 1555 1555 3.19 SITE 1 AC1 2 SER A 207 HIS A 237 SITE 1 AC2 2 TYR A 63 GLY A 64 CRYST1 51.087 51.077 85.378 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 0.019574 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019578 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011713 0.00000