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

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Basic information

Entry
Database: PDB / ID: 4wfj
TitleCrystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 1.75 angstrom resolution
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: 1.75 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 1.1May 20, 2015Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
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_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3633
Polymers30,2881
Non-polymers762
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.560, 65.840, 70.080
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium fluoride, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 47777 / % possible obs: 99.8 % / Redundancy: 7.4 % / Net I/σ(I): 26.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 1.75→19.553 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1301 5.12 %
Rwork0.2026 --
obs0.2047 25414 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072065
X-RAY DIFFRACTIONf_angle_d1.0952811
X-RAY DIFFRACTIONf_dihedral_angle_d11.854761
X-RAY DIFFRACTIONf_chiral_restr0.044302
X-RAY DIFFRACTIONf_plane_restr0.007372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.25011520.21962705X-RAY DIFFRACTION100
1.82-1.90280.34541380.29682523X-RAY DIFFRACTION94
1.9028-2.0030.45631320.39152287X-RAY DIFFRACTION85
2.003-2.12840.25111170.22232756X-RAY DIFFRACTION100
2.1284-2.29250.28511740.21462681X-RAY DIFFRACTION100
2.2925-2.52280.23321360.20462747X-RAY DIFFRACTION100
2.5228-2.88680.29421490.20292757X-RAY DIFFRACTION100
2.8868-3.63330.22171470.1842746X-RAY DIFFRACTION99
3.6333-19.55380.17831560.15592911X-RAY DIFFRACTION100

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