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Yorodumi- PDB-5v26: 1.78 angstrom crystal structure of P97H 3-hydroxyanthranilate-3,4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v26 | |||||||||
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Title | 1.78 angstrom crystal structure of P97H 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans | |||||||||
Components | 3-hydroxyanthranilate 3,4-dioxygenase | |||||||||
Keywords | OXIDOREDUCTASE / HAO Kynurenine Cupin Dioxygenase | |||||||||
Function / homology | Function and homology information 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / quinolinate biosynthetic process / anthranilate metabolic process / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / ferrous iron binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Cupriavidus metallidurans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | |||||||||
Authors | Dornevil, K. / Liu, F. / Liu, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: 1.78 angstrom crystal structure of P97H 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans Authors: Dornevil, K. / Liu, F. / Liu, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v26.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v26.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 5v26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/5v26 ftp://data.pdbj.org/pub/pdb/validation_reports/v2/5v26 | HTTPS FTP |
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-Related structure data
Related structure data | 1yfuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23120.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34) (bacteria) Strain: ATCC 43123 / DSM 2839 / NBRC 102507 / CH34 / Gene: nbaC, Rmet_5193 / Production host: Escherichia coli (E. coli) References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase #2: Chemical | ChemComp-FE2 / #3: 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: 2.18 Å3/Da / Density % sol: 43.53 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris-HCl, 200 mM MgCl2, 20% PEG 8000, and 1 mM DTT, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→50 Å / Num. obs: 37328 / % possible obs: 98.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 26.59 Å2 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.05 / Rrim(I) all: 0.139 / Χ2: 1.133 / Net I/σ(I): 5.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YFU Resolution: 1.79→38.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.84 Å2 / Biso mean: 35.3916 Å2 / Biso min: 17.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.79→38.6 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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