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Yorodumi- PDB-8h5j: Crystal structure of PETase S121E/A180V/P181V/D186H/N233C/S242T/N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h5j | ||||||
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Title | Crystal structure of PETase S121E/A180V/P181V/D186H/N233C/S242T/N246D/S282C mutant from Ideonella sakaiensis | ||||||
Components | Poly(ethylene terephthalate) hydrolase | ||||||
Keywords | HYDROLASE / PET hydrolase / Ideonella sakaiensis / 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: 1.4 Å | ||||||
Authors | Lee, S.H. / Seo, H. / Kim, K.-J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: A case of balance engineering exhibits kinetic relationship between mesophilic and thermophilic poly(ethylene terephthalate) depolymerases. Authors: Lee, S.H. / Seo, H. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h5j.cif.gz | 129.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h5j.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 8h5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/8h5j ftp://data.pdbj.org/pub/pdb/validation_reports/h5/8h5j | HTTPS FTP |
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-Related structure data
Related structure data | 8h5kC 8h5lC 8h5mC 8h5oC 5xjhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 31606.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 1.86 Å3/Da / Density % sol: 33.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 25 % PEG3350, 0.1 M BIS-TRIS pH6.5, and 0.2 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→28.65 Å / Num. obs: 88810 / % possible obs: 98.3 % / Redundancy: 1.6 % / CC1/2: 0.984 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 4312 / CC1/2: 0.736 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XJH Resolution: 1.4→28.65 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.148 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.44 Å2 / Biso mean: 17.278 Å2 / Biso min: 9.8 Å2
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Refinement step | Cycle: final / Resolution: 1.4→28.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.404→1.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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