+Open data
-Basic information
Entry | Database: PDB / ID: 8h81 | ||||||
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Title | Trans-3/4-proline-hydroxylase H11 with 4-Hydroxyl-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 / 4-HYDROXYPROLINE / Phytanoyl-CoA dioxygenase Function and homology information | ||||||
Biological species | uncultured bacterium esnapd13 (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 | 8h81.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h81.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 8h81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/8h81 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/8h81 | HTTPS FTP |
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-Related structure data
Related structure data | 8h7tC 8h7vC 8h7yC 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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Unit cell |
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-Components
#1: Protein | Mass: 29867.504 Da / Num. of mol.: 1 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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#2: Chemical | ChemComp-HYP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 64.13 % |
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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→75.29 Å / Num. obs: 36880 / % possible obs: 99.9 % / Redundancy: 24.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.012 / Rrim(I) all: 0.059 / Χ2: 0.843 / Net I/σ(I): 152.6 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 25.1 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 1801 / CC1/2: 0.97 / CC star: 0.992 / Rpim(I) all: 0.107 / Rrim(I) all: 0.54 / Χ2: 0.46 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LNS 6lns Resolution: 1.84→24.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.308 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.088 / 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: 130.04 Å2 / Biso mean: 36.834 Å2 / Biso min: 14.9 Å2
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Refinement step | Cycle: final / Resolution: 1.84→24.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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