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Yorodumi- PDB-4r52: 1.5 angstrom crystal structure of 3-hydroxyanthranilate-3,4-dioxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r52 | ||||||
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Title | 1.5 angstrom crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans | ||||||
Components | 3-hydroxyanthranilate 3,4-dioxygenaseHAAO | ||||||
Keywords | OXIDOREDUCTASE / Cupin Rubredoxin | ||||||
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 Similarity search - Function | ||||||
Biological species | Cupriavidus metallidurans CH34 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Geng, J. / Gumpper, R.H. / Huo, L. / Liu, A. | ||||||
Citation | Journal: To be Published Title: 1.5 angstrom crystal structure of 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans Authors: Geng, J. / Gumpper, R.H. / Huo, L. / Liu, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r52.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r52.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 4r52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/4r52 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/4r52 | 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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Unit cell |
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-Components
#1: Protein | Mass: 20056.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus metallidurans CH34 (bacteria) Strain: CH34 / Gene: nbaC, nbaC Rmet_5193, Rmet_5193 / Plasmid: PET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase | ||||
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#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 8000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. all: 36578 / Num. obs: 36541 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 59.1 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 22.8 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1755 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YFU Resolution: 1.53→49.349 Å / SU ML: 0.18 / σ(F): 0.21 / Phase error: 22.15 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.766 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.53→49.349 Å
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Refine LS restraints |
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LS refinement shell |
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