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Yorodumi- PDB-5xg0: Crystal structure of a novel PET hydrolase from Ideonella sakaien... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xg0 | ||||||
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Title | Crystal structure of a novel PET hydrolase from Ideonella sakaiensis 201-F6 | ||||||
Components | Poly(ethylene terephthalate) hydrolase | ||||||
Keywords | HYDROLASE / metal-binding / substrate binding / acidocalcisomal pyrophosphatase / inhibitor | ||||||
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 / molecular replacement / Resolution: 1.58 Å | ||||||
Authors | Han, X. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structural insight into catalytic mechanism of PET hydrolase Authors: Han, X. / Liu, W. / Huang, J.W. / Ma, J. / Zheng, Y. / Ko, T.P. / Xu, L. / Cheng, Y.S. / Chen, C.C. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xg0.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xg0.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/5xg0 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/5xg0 | HTTPS FTP |
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-Related structure data
Related structure data | 5xfyC 5xfzC 5xh2C 5xh3C 4wfiS 5xfx C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 27866.930 Da / Num. of mol.: 3 / Fragment: UNP residues 30-290 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria) Strain: 201-F6 / Gene: ISF6_4831 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase #2: Water | ChemComp-HOH / | |
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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: 2.01 Å3/Da / Density % sol: 38.83 % / Mosaicity: 0.29 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Polyethylene Glycol 6000, Glycerol, MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 29, 2016 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→25 Å / Num. obs: 92787 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.018 / Rrim(I) all: 0.043 / Χ2: 1.54 / Net I/σ(I): 32.2 / Num. measured all: 499698 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.076 / Num. unique obs: 9169 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Χ2: 1.74 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WFI Resolution: 1.58→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.085 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.073 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: 81.08 Å2 / Biso mean: 11.229 Å2 / Biso min: 1 Å2
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Refinement step | Cycle: final / Resolution: 1.58→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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