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Yorodumi- PDB-5xfz: Crystal structure of a novel PET hydrolase R103G/S131A mutant fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xfz | ||||||
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Title | Crystal structure of a novel PET hydrolase R103G/S131A mutant 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 / Resolution: 1.55 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 | 5xfz.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xfz.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/5xfz ftp://data.pdbj.org/pub/pdb/validation_reports/xf/5xfz | HTTPS FTP |
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-Related structure data
Related structure data | 5xfyC 5xg0C 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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Unit cell |
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-Components
#1: Protein | Mass: 27366.400 Da / Num. of mol.: 1 / Fragment: UNP residues 30-290 / Mutation: R103G, S131A 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 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.03 Å3/Da / Density % sol: 39.47 % / Mosaicity: 0.465 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium Sulfate, NaCl, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→25 Å / Num. obs: 33154 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.039 / Rrim(I) all: 0.086 / Χ2: 0.85 / Net I/σ(I): 7.7 / Num. measured all: 157183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WFI Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.343 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071 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: 77.92 Å2 / Biso mean: 13.725 Å2 / Biso min: 6.71 Å2
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Refinement step | Cycle: final / Resolution: 1.55→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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