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- PDB-4wfi: Crystal structure of PET-degrading cutinase Cut190 S226P mutant i... -

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Basic information

Entry
Database: PDB / ID: 4wfi
TitleCrystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-free state
ComponentsCutinase
KeywordsHYDROLASE / Cutinase / Polyesterase / alpha/beta-hydrolase fold
Function / homology
Function and homology information


cutinase / carboxylic ester hydrolase activity / metal ion binding
Similarity search - Function
Platelet-activating factor acetylhydrolase, isoform II / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.446 Å
AuthorsMiyakawa, T. / Mizushima, H. / Ohtsuka, J. / Oda, M. / Kawai, F. / Tanokura, M.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190.
Authors: Miyakawa, T. / Mizushima, H. / Ohtsuka, J. / Oda, M. / Kawai, F. / Tanokura, M.
History
DepositionSep 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Structure summary
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)30,2881
Polymers30,2881
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.447, 65.142, 69.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cutinase /


Mass: 30287.916 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 47-304 / Mutation: S226P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Strain: AHK190 / Gene: Cut190 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) / References: UniProt: W0TJ64
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM Bis-Tris, 50 mM ammonium sulfate, 25% (w/v) pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.446→20 Å / Num. obs: 47285 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 74.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 1.446→19.498 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1913 2381 5.05 %
Rwork0.1756 --
obs0.1764 47174 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.446→19.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 226 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062065
X-RAY DIFFRACTIONf_angle_d1.0692811
X-RAY DIFFRACTIONf_dihedral_angle_d10.894761
X-RAY DIFFRACTIONf_chiral_restr0.044302
X-RAY DIFFRACTIONf_plane_restr0.006372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4461-1.47560.23571290.20032501X-RAY DIFFRACTION95
1.4756-1.50770.24361390.18422593X-RAY DIFFRACTION100
1.5077-1.54280.2261470.18612579X-RAY DIFFRACTION100
1.5428-1.58130.23221390.18322633X-RAY DIFFRACTION100
1.5813-1.62410.21321230.1792601X-RAY DIFFRACTION100
1.6241-1.67180.20671440.17022631X-RAY DIFFRACTION100
1.6718-1.72580.17941420.17242590X-RAY DIFFRACTION100
1.7258-1.78740.22341500.17512622X-RAY DIFFRACTION100
1.7874-1.85890.19521360.17262631X-RAY DIFFRACTION100
1.8589-1.94350.19711440.17242618X-RAY DIFFRACTION100
1.9435-2.04580.20581450.16842626X-RAY DIFFRACTION100
2.0458-2.17380.18191240.17212670X-RAY DIFFRACTION100
2.1738-2.34140.18241280.16672648X-RAY DIFFRACTION100
2.3414-2.57660.19411620.17012652X-RAY DIFFRACTION100
2.5766-2.94830.18641560.17482646X-RAY DIFFRACTION100
2.9483-3.71040.18481310.17632727X-RAY DIFFRACTION100
3.7104-19.49940.17491420.16812825X-RAY DIFFRACTION99

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