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Yorodumi- PDB-8h83: Crystal structure of a IsPETase variant V22 from Ideonella sakaiensis -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h83 | ||||||
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Title | Crystal structure of a IsPETase variant V22 from Ideonella sakaiensis | ||||||
Components | Poly(ethylene terephthalate) hydrolase | ||||||
Keywords | HYDROLASE / PET degradation / mutant | ||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / : / xenobiotic catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Ideonella sakaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Wei, H.L. / Gao, S.F. / Li, Q. / Han, X. / Gao, J. / Liu, W.D. | ||||||
Funding support | China, 1items
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Citation | Journal: to be published Title: Crystal structure of a IsPETase variant V22 from Ideonella sakaiensis Authors: Wei, H.L. / Gao, S.F. / Li, Q. / Han, X. / Gao, J. / Liu, W.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h83.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h83.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 8h83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/8h83 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/8h83 | HTTPS FTP |
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-Related structure data
Related structure data | 5xh3S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1
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-Components
#1: Protein | Mass: 34634.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Strain: NBRC 110686 / TISTR 2288 / 201-F6 / Gene: ISF6_4831 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (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: 2.01 Å3/Da / Density % sol: 38.8 % / Mosaicity: 0.851 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0 M sodium citrate, 0.1 M Imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→50 Å / Num. obs: 43072 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 23.79 Å2 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.062 / Rrim(I) all: 0.227 / Χ2: 0.959 / Net I/σ(I): 3.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XH3 Resolution: 1.92→47.89 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.01 Å2 / Biso mean: 24.4271 Å2 / Biso min: 12.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→47.89 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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