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- PDB-8ibm: Sulfate bound form of PET-degrading cutinase Cut190 with thermost... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ibm | ||||||
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Title | Sulfate bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation | ||||||
![]() | Alpha/beta hydrolase family protein | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Emori, M. / Numoto, N. / Kamiya, N. / Oda, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120 KB | Display | ![]() |
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PDB format | ![]() | 86.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iblC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.8 % |
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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: ![]() ![]() ![]() |
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: 2.2→37 Å / Num. obs: 25685 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 38.44 Å2 / CC1/2: 0.997 / Rsym value: 0.125 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4113 / CC1/2: 0.743 / Rsym value: 1.46 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 48.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→36.27 Å
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Refine LS restraints |
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LS refinement shell |
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