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Yorodumi- PDB-7ctr: Closed form of PET-degrading cutinase Cut190 with thermostability... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ctr | ||||||
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Title | Closed form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H | ||||||
Components | Alpha/beta hydrolase family protein | ||||||
Keywords | HYDROLASE / PROTEIN ENGINEERING / POLYESTERASE / disulfide bond / metal binding | ||||||
Function / homology | Platelet-activating factor acetylhydrolase, isoform II / cutinase / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / 1,4-DIETHYLENE DIOXIDE / cutinase Function and homology information | ||||||
Biological species | Saccharomonospora viridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Emori, M. / Numoto, N. / Senga, A. / Bekker, G.J. / Kamiya, N. / Ito, N. / Kawai, F. / Oda, M. | ||||||
Citation | Journal: Proteins / Year: 2021 Title: Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability. Authors: Emori, M. / Numoto, N. / Senga, A. / Bekker, G.J. / Kamiya, N. / Kobayashi, Y. / Ito, N. / Kawai, F. / Oda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ctr.cif.gz | 267.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ctr.ent.gz | 189.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ctr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ctr_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 7ctr_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 7ctr_validation.xml.gz | 26 KB | Display | |
Data in CIF | 7ctr_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/7ctr ftp://data.pdbj.org/pub/pdb/validation_reports/ct/7ctr | HTTPS FTP |
-Related structure data
Related structure data | 7ctsC 4wfiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28905.537 Da / Num. of mol.: 2 / Mutation: S226P, R228S, Q138A, D250C, E296C, Q123H, N202H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Gene: Cut190, SAMN02982918_2340 / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA-GAMI B (DE3) / References: UniProt: W0TJ64, cutinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 45% (v/v) 1,4-dioxane |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→43 Å / Num. obs: 144266 / % possible obs: 96.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 12.21 Å2 / CC1/2: 0.998 / Rsym value: 0.179 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.2→1.27 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 22418 / CC1/2: 0.693 / Rsym value: 1.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WFI Resolution: 1.2→42.78 Å / SU ML: 0.137 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4597 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→42.78 Å
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Refine LS restraints |
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LS refinement shell |
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