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Yorodumi- PDB-8ibl: MES bound form of PET-degrading cutinase Cut190 with thermostabil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ibl | ||||||
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Title | MES bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | ||||||
Components | Alpha/beta hydrolase family protein | ||||||
Keywords | HYDROLASE / PROTEIN ENGINEERING / POLYESTERASE / DISULFIDE BOND / METAL BINDING / Ligand complex | ||||||
Function / homology | Platelet-activating factor acetylhydrolase, isoform II / cutinase / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / cutinase Function and homology information | ||||||
Biological species | Saccharomonospora viridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Emori, M. / Numoto, N. / Kamiya, N. / Oda, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biorxiv / Year: 2023 Title: Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism. Authors: Numoto, N. / Kamiya, N. / Oda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ibl.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ibl.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ibl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ibl_validation.pdf.gz | 970.2 KB | Display | wwPDB validaton report |
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Full document | 8ibl_full_validation.pdf.gz | 963.8 KB | Display | |
Data in XML | 8ibl_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 8ibl_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/8ibl ftp://data.pdbj.org/pub/pdb/validation_reports/ib/8ibl | HTTPS FTP |
-Related structure data
Related structure data | 8ibmC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 28889.537 Da / Num. of mol.: 2 Mutation: Q123H,Q138A, S176A, N202H, S226P, R228S, D250C, E296C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Gene: Cut190, SAMN02982918_2340 / Production host: Escherichia coli (E. coli) / References: UniProt: W0TJ64, cutinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.27 Å3/Da / Density % sol: 45.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES monohydrate pH 6.5, 0.2 M Ammonium sulfate, and 30% (w/v) PEG MME 5,000 |
-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: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→33 Å / Num. obs: 15681 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 36.34 Å2 / CC1/2: 0.98 / Rsym value: 0.276 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.61→2.76 Å / Num. unique obs: 2506 / CC1/2: 0.642 / Rsym value: 1.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→32.36 Å / SU ML: 0.3911 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.2956 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 36.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→32.36 Å
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Refine LS restraints |
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LS refinement shell |
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