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- PDB-7e00: Trans-proline-hydroxylase H11 with Succinic and L-proline in the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7 | ||||||
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Title | Trans-proline-hydroxylase H11 with Succinic and L-proline in the fourth reaction state. | ||||||
![]() | Phytanoyl-CoA dioxygenase | ||||||
![]() | HYDROLASE / L-proline / Trans / Hydroxylase / AKG / mutant | ||||||
Function / homology | phytanoyl-CoA dioxygenase activity / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / metal ion binding / 2-OXOGLUTARIC ACID / OXYGEN ATOM / PROLINE / SUCCINIC ACID / Phytanoyl-CoA dioxygenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gong, W.G. / Yang, L.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Trans-3/4-proline-hydroxylase H11 with AKG and L-proline 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 | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 95.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dt0SC ![]() 7e05C ![]() 7e06C ![]() 7e07C ![]() 7e09C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30108.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 242 molecules ![](data/chem/img/PRO.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/O.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/O.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-AKG / | #5: Chemical | ChemComp-O / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.61 % |
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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: 1.92→85.54 Å / Num. obs: 63525 / % possible obs: 99.2 % / Redundancy: 13 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.92→2.02 Å / Rmerge(I) obs: 1.218 / Num. unique obs: 9204 / Rpim(I) all: 0.351 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DT0 Resolution: 1.92→85.54 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 118.7 Å2 / Biso mean: 39.3576 Å2 / Biso min: 17.85 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→85.54 Å
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