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Yorodumi- PDB-5yns: Crystal structure of PETase R280A mutant from Ideonella sakaiensis -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yns | ||||||
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Title | Crystal structure of PETase R280A 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 / : / xenobiotic catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Ideonella sakaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Joo, S. / Kim, K.-J. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation. Authors: Joo, S. / Cho, I.J. / Seo, H. / Son, H.F. / Sagong, H.-Y. / Shin, T.J. / 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 | 5yns.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yns.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yns_validation.pdf.gz | 417.9 KB | Display | wwPDB validaton report |
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Full document | 5yns_full_validation.pdf.gz | 418.2 KB | Display | |
Data in XML | 5yns_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5yns_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/5yns ftp://data.pdbj.org/pub/pdb/validation_reports/yn/5yns | HTTPS FTP |
-Related structure data
Related structure data | 5xjhSC 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: 27590.596 Da / Num. of mol.: 1 / Fragment: a/b hydrolase superfamily / Mutation: R280A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria) Strain: 201-F6 / Gene: ISF6_4831 / 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: 2.59 Å3/Da / Density % sol: 52.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: BIS-Tris, Ammonium acetate, PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Oct 24, 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: 1.36→50 Å / Num. obs: 62494 / % possible obs: 98.7 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 40.79 |
Reflection shell | Rmerge(I) obs: 0.374 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XJH Resolution: 1.36→27.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.858 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.052 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.25 Å2 / Biso mean: 14.344 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 1.36→27.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.396 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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