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HEADER HYDROLASE 20-OCT-18 6ILX
TITLE CRYSTAL STRCUTURE 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 1 27-MAR-19 6ILX 0
JRNL AUTH C.C.LIU,C.SHI
JRNL TITL CRYSTAL STRCUTURE OF PETASE W159F MUTANT FROM IDEONELLA
JRNL TITL 2 SAKAIENSIS
JRNL REF TO BE PUBLISHED
JRNL REFN
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
TER 1953 HIS A 293
MASTER 254 0 2 9 9 0 2 6 2093 1 7 21
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