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Yorodumi- PDB-5iat: Mechanistic and Structural Analysis of Substrate Recognition and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iat | ||||||
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Title | Mechanistic and Structural Analysis of Substrate Recognition and Cofactor Binding by an Unusual Bacterial Prolyl Hydroxylase - apo-BaP4H | ||||||
Components | Procollagen-Proline Dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / P4H / Dioxygenase / Cupin / Fe(II)/alpha-ketoglutarate | ||||||
Function / homology | Function and homology information procollagen-proline 4-dioxygenase activity / L-ascorbic acid binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å | ||||||
Authors | Schnicker, N.J. / Dey, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Bacillus anthracis Prolyl 4-Hydroxylase Modifies Collagen-like Substrates in Asymmetric Patterns. Authors: Schnicker, N.J. / Dey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iat.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iat.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 5iat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/5iat ftp://data.pdbj.org/pub/pdb/validation_reports/ia/5iat | HTTPS FTP |
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-Related structure data
Related structure data | 5iavC 5iaxC 3itqS 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
#1: Protein | Mass: 24708.592 Da / Num. of mol.: 2 / Fragment: UNP residues 18-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BASH2_01493 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7R8C5, UniProt: A0A4Y1WAP5*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 40 mM KH2PO4 pH 6, 14 % PEG 8000, 20 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jun 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→33.28 Å / Num. obs: 50418 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 6990 / % possible all: 96.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ITQ Resolution: 1.67→33.279 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.33 Å2 / Biso mean: 23.4144 Å2 / Biso min: 6.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.67→33.279 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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