+Open data
-Basic information
Entry | Database: PDB / ID: 8h7y | ||||||
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Title | Trans-3/4-proline-hydroxylase H11 with AKG and L-proline | ||||||
Components | Phytanoyl-CoA dioxygenase | ||||||
Keywords | STRUCTURAL PROTEIN / L-proline / Trans / Hydroxylase / AKG / HYDROLASE | ||||||
Function / homology | Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / 2-OXOGLUTARIC ACID / : / PROLINE / Phytanoyl-CoA dioxygenase Function and homology information | ||||||
Biological species | uncultured bacterium esnapd13 (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Gong, W.M. / Hu, X.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Structures of L-proline trans-hydroxylase reveal the catalytic specificity and provide deeper insight into AKG-dependent hydroxylation. Authors: Hu, X. / Huang, X. / Liu, J. / Zheng, P. / Gong, W. / Yang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h7y.cif.gz | 236.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h7y.ent.gz | 192.5 KB | Display | PDB format |
PDBx/mmJSON format | 8h7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/8h7y ftp://data.pdbj.org/pub/pdb/validation_reports/h7/8h7y | HTTPS FTP |
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-Related structure data
Related structure data | 8h7tC 8h7vC 8h81C 8h85C 6lns S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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 | #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: 3.4 Å3/Da / Density % sol: 63.87 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.7M Sodium citrate tribasic dihydrate and 0.1M 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: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.139→85.81 Å / Num. obs: 44086 / % possible obs: 94.46 % / Redundancy: 28.6 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.025 / Rrim(I) all: 0.135 / Χ2: 3.133 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.14→2.18 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2262 / CC1/2: 0.981 / CC star: 0.995 / Rpim(I) all: 0.1 / Rrim(I) all: 0.538 / Χ2: 1.419 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LNS 6lns Resolution: 2.14→39.79 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.184 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 36.658 Å2
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Refinement step | Cycle: 1 / Resolution: 2.14→39.79 Å
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