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Yorodumi- PDB-6ij3: Crystal structure of PETase S121D, D186H mutant from Ideonella sa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ij3 | ||||||
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Title | Crystal structure of PETase S121D, D186H mutant from Ideonella sakaiensis | ||||||
Components | Poly(ethylene terephthalate) hydrolase | ||||||
Keywords | HYDROLASE | ||||||
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: 1.4 Å | ||||||
Authors | Joo, S. / Kim, K.J. | ||||||
Citation | Journal: Acs Catalysis / Year: 2019 Title: Rational Protein Engineering of Thermo-Stable PETase from Ideonella sakaiensis for Highly Efficient PET Degradation Authors: Son, H.F. / Cho, I.J. / Joo, S. / Seo, H. / Sagong, H.Y. / Choi, S.Y. / Lee, S.Y. / 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 | 6ij3.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ij3.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ij3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/6ij3 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/6ij3 | HTTPS FTP |
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-Related structure data
Related structure data | 6ij4C 6ij5C 6ij6C 5xjhS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 31570.064 Da / Num. of mol.: 1 / Mutation: S121D, D186H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami-b References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase |
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#2: 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: 1.92 Å3/Da / Density % sol: 35.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Tris, PEG 3000, NaCl |
-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: Jul 23, 2017 |
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→50 Å / Num. obs: 46596 / % possible obs: 99 % / Redundancy: 3.2 % / Rpim(I) all: 0.067 / Net I/σ(I): 25.99 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 2301 / Rpim(I) all: 0.215 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XJH Resolution: 1.4→21.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.399 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.447 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→21.61 Å
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Refine LS restraints |
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