+Open data
-Basic information
Entry | Database: PDB / ID: 6ilw | |||||||||
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Title | Crystal structure of PETase from Ideonella sakaiensis | |||||||||
Components | Poly(ethylene terephthalate) hydrolase | |||||||||
Keywords | HYDROLASE / Crystal strcuture of PETase from Ideonella sakaiensis | |||||||||
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: 1.575 Å | |||||||||
Authors | Liu, C.C. / Shi, C. | |||||||||
Funding support | China, 2items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Structural and functional characterization of polyethylene terephthalate hydrolase from Ideonella sakaiensis. Authors: Liu, C. / Shi, C. / Zhu, S. / Wei, R. / Yin, C.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ilw.cif.gz | 117.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ilw.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ilw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/6ilw ftp://data.pdbj.org/pub/pdb/validation_reports/il/6ilw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28540.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria) Strain: 201-F6 / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.68 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris, pH 5.5, 3M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9776 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9776 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 31751 / % possible obs: 94.6 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.011 / Rrim(I) all: 0.038 / Rsym value: 0.033 / Χ2: 0.881 / Net I/σ(I): 59.37 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 14.8 / Num. unique obs: 1630 / CC1/2: 0.991 / Rpim(I) all: 0.052 / Rrim(I) all: 0.181 / Rsym value: 0.159 / Χ2: 0.936 / % possible all: 49.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.575→44.079 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.575→44.079 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.9637 Å / Origin y: 0.5874 Å / Origin z: 6.8599 Å
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Refinement TLS group | Selection details: all |