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Yorodumi- PDB-7e00: Trans-proline-hydroxylase H11 with Succinic and L-proline in the ... -
+Open data
-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. | ||||||
Components | Phytanoyl-CoA dioxygenase | ||||||
Keywords | HYDROLASE / L-proline / Trans / Hydroxylase / AKG / mutant | ||||||
Function / homology | Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / 2-OXOGLUTARIC ACID / 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: 1.92 Å | ||||||
Authors | Gong, W.G. / Yang, L.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e00.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e00.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 7e00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/7e00 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/7e00 | HTTPS FTP |
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-Related structure data
Related structure data | 7dt0SC 7e05C 7e06C 7e07C 7e09C S: Starting model for refinement C: citing same article (ref.) |
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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
-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.) uncultured bacterium esnapd13 (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: S5TUM1 |
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-Non-polymers , 5 types, 242 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 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: 1.92→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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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