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Open data
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Basic information
Entry | Database: PDB / ID: 7dzz | ||||||
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Title | Trans-3/4-proline-hydroxylase H11-stateV | ||||||
![]() | Phytanoyl-CoA dioxygenase | ||||||
![]() | HYDROLASE / L-proline / hydroxylase / reaction intermediate / succinic | ||||||
Function / homology | phytanoyl-CoA dioxygenase activity / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / metal ion binding / OXYGEN ATOM / PROLINE / SUCCINIC ACID / Phytanoyl-CoA dioxygenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gong, W.G. / Yang, L.Y. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.1 KB | Display | ![]() |
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PDB format | ![]() | 95 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dt0S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Production host: ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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