+Open data
-Basic information
Entry | Database: PDB / ID: 7dzz | ||||||
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Title | Trans-3/4-proline-hydroxylase H11-stateV | ||||||
Components | Phytanoyl-CoA dioxygenase | ||||||
Keywords | HYDROLASE / L-proline / hydroxylase / reaction intermediate / succinic | ||||||
Function / homology | Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / OXYGEN ATOM / PROLINE / SUCCINIC ACID / Phytanoyl-CoA dioxygenase Function and homology information | ||||||
Biological species | uncultured bacterium esnapd13 (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Gong, W.G. / Yang, L.Y. | ||||||
Citation | Journal: To Be Published Title: Trans-3/4-proline-hydroxylase H11-stateV Authors: Gong, W.G. / Yang, L.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dzz.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dzz.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 7dzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/7dzz ftp://data.pdbj.org/pub/pdb/validation_reports/dz/7dzz | HTTPS FTP |
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-Related structure data
Related structure data | 7dt0S 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: 30108.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium esnapd13 (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: S5TUM1 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-O / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.43 Å3/Da / Density % sol: 64.19 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.7 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→85.69 Å / Num. obs: 56700 / % possible obs: 92.5 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.95→2.05 Å / Rmerge(I) obs: 1.207 / Num. unique obs: 8808 / Rsym value: 0.346 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DT0 Resolution: 1.95→85.69 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.591 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.4 Å2 / Biso mean: 44.203 Å2 / Biso min: 19.51 Å2
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Refinement step | Cycle: final / Resolution: 1.95→85.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→1.997 Å / Rfactor Rfree error: 0
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