+Open data
-Basic information
Entry | Database: PDB / ID: 6ky5 | ||||||
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Title | Crystal structure of a hydrolase mutant | ||||||
Components | PET hydrolase | ||||||
Keywords | HYDROLASE / PET hydrolase / mutant | ||||||
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: 1.631 Å | ||||||
Authors | Cui, Y.L. / Chen, Y.C. / Liu, X.Y. / Dong, S.J. / Han, J. / Xiang, H. / Chen, Q. / Liu, H.Y. / Han, X. / Liu, W.D. ...Cui, Y.L. / Chen, Y.C. / Liu, X.Y. / Dong, S.J. / Han, J. / Xiang, H. / Chen, Q. / Liu, H.Y. / Han, X. / Liu, W.D. / Tang, S.Y. / Wu, B. | ||||||
Funding support | China, 1items
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Citation | Journal: Biorxiv / Year: 2020 Title: Computational redesign of PETase for plasticbiodegradation by GRAPE strategy. Authors: Cui, Y.L. / Chen, Y.C. / Liu, X.Y. / Dong, S.J. / Tian, Y. / Qiao, Y.X. / Mitra, R. / Han, J. / Li, C.L. / Han, X. / Liu, W.D. / Chen, Q. / Du, W.B. / Tang, S.Y. / Xiang, H. / Liu, H.Y. / Wu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ky5.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ky5.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ky5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ky5_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 6ky5_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | 6ky5_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 6ky5_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/6ky5 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/6ky5 | HTTPS FTP |
-Related structure data
Related structure data | 5xh3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 29 - 292 / Label seq-ID: 29 - 292
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-Components
#1: Protein | Mass: 31483.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0K8P6T7*PLUS #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.34 Å3/Da / Density % sol: 47.33 % / Mosaicity: 0.947 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 30, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.63→25 Å / Num. obs: 71809 / % possible obs: 96.6 % / Redundancy: 9 % / Biso Wilson estimate: 22.61 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Rrim(I) all: 0.067 / Χ2: 0.854 / Net I/σ(I): 14.6 / Num. measured all: 644782 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XH3 Resolution: 1.631→24.887 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.35 Å2 / Biso mean: 25.6233 Å2 / Biso min: 12.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.631→24.887 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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