+Open data
-Basic information
Entry | Database: PDB / ID: 5xjh | ||||||
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Title | Crystal structure of PETase 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: 1.54 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 | 5xjh.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xjh.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 5xjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/5xjh ftp://data.pdbj.org/pub/pdb/validation_reports/xj/5xjh | HTTPS FTP |
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-Related structure data
Related structure data | 5ynsC 3visS 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: 31490.912 Da / Num. of mol.: 1 / Fragment: a/b hydrolase superfamily, UNP residues 34-290 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (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: 2.25 Å3/Da / Density % sol: 45.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: BIS-Tris, Ammonium acetate, PEG 10000 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.55→50 Å / Num. obs: 42939 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 31.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.55→1.58 Å / % possible obs: 99.9 % / Redundancy: 6.5 % / Rsym value: 0.296 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VIS Resolution: 1.54→29.343 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.093 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.068 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: 65.02 Å2 / Biso mean: 16.121 Å2 / Biso min: 2.17 Å2
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Refinement step | Cycle: final / Resolution: 1.54→29.343 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.541→1.581 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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