+Open data
-Basic information
Entry | Database: PDB / ID: 8j17 | |||||||||
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Title | Crystal structure of IsPETase variant | |||||||||
Components | Poly(ethylene terephthalate) hydrolase | |||||||||
Keywords | HYDROLASE / polyethylene terephthalate (PET) / IsPETase / PET degradation | |||||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / cellular response to organic substance / xenobiotic catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Ideonella sakaiensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | |||||||||
Authors | Yin, Q.D. / Wang, Y.X. | |||||||||
Funding support | China, 2items
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Citation | Journal: Green Chem / Year: 2013 Title: Efficient polyethylene terephthalate biodegradation by an engineered Ideonella sakaiensis PETase with a fixed substrate-binding W156 residue Authors: Yin, Q. / Zhang, J. / Ma, S. / Gu, T. / Wang, M. / You, S. / Ye, S. / Su, R. / Wang, Y. / Qi, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j17.cif.gz | 174 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j17.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 8j17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/8j17 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/8j17 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28748.943 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase #2: Water | ChemComp-HOH / | |
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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: 2.92 Å3/Da / Density % sol: 57.81 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100mM MES-NaOH, 1.7M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→58.45 Å / Num. obs: 71765 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 37.3 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.97→2.02 Å / Num. unique obs: 5267 / CC1/2: 0.672 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→40.92 Å / SU ML: 0.216 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9067 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: 43.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→40.92 Å
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Refine LS restraints |
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LS refinement shell |
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