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Yorodumi- PDB-7ec8: Polyethylene terephthalate hydrolyzing lipase PET2 mutant - F105R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ec8 | ||||||
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Title | Polyethylene terephthalate hydrolyzing lipase PET2 mutant - F105R-E110K | ||||||
Components | LipIAF5-2 | ||||||
Keywords | HYDROLASE / Polyethylene terephthalate hydrolase / lipase | ||||||
Function / homology | Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold / hydrolase activity / LipIAF5-2 Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Nakamura, A. | ||||||
Citation | Journal: Acs Catalysis / Year: 2021 Title: Positive Charge Introduction on the Surface of Thermostabilized PET Hydrolase Facilitates PET Binding and Degradation. Authors: Nakamura, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ec8.cif.gz | 131 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ec8.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ec8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/7ec8 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/7ec8 | HTTPS FTP |
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-Related structure data
-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: 31610.246 Da / Num. of mol.: 2 / Mutation: F105R, E110K Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: lipIAF5-2 / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / References: UniProt: C3RYL0 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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 Å3/Da / Density % sol: 38.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M ammonium sulfate in 100 mM Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→33.4 Å / Num. obs: 111811 / % possible obs: 99.5 % / Redundancy: 13.9 % / Biso Wilson estimate: 13.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 17635 / CC1/2: 0.772 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→33.4 Å / SU ML: 0.1685 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.3612 / Stereochemistry target values: GeoStd + Monomer Library
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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: 17.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→33.4 Å
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Refine LS restraints |
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LS refinement shell |
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