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Yorodumi- PDB-3fe5: Crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fe5 | ||||||
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Title | Crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from bovine kidney | ||||||
Components | 3-hydroxyanthranilate 3,4-dioxygenaseHAAO | ||||||
Keywords | OXIDOREDUCTASE / CUPIN / 3HAO / Quinolinic acid / Cytoplasm / Dioxygenase / Iron / Metal-binding | ||||||
Function / homology | Function and homology information Tryptophan catabolism / quinolinate metabolic process / 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 / NAD biosynthetic process / ferrous iron binding ...Tryptophan catabolism / quinolinate metabolic process / 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 / NAD biosynthetic process / ferrous iron binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Dilovic, I. / Gliubich, F. / Malpeli, G. / Zanotti, G. / Matkovic-Calogovic, D. | ||||||
Citation | Journal: Biopolymers / Year: 2009 Title: Crystal structure of bovine 3-hydroxyanthranilate 3,4-dioxygenase. Authors: Dilovic, I. / Gliubich, F. / Malpeli, G. / Zanotti, G. / Matkovic-Calogovic, D. #1: Journal: Biochemistry / Year: 2005 Title: Structural studies on 3-hydroxyanthranilate-3,4-dioxygenase: the catalytic mechanism of a complex oxidation involved in NAD biosynthesis. Authors: Zhang, Y. / Colabroy, K.L. / Begley, T.P. / Ealick, S.E. #2: Journal: Protein Sci. / Year: 2006 Title: Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: a special subgroup of the type III extradiol dioxygenases. Authors: Li, X. / Guo, M. / Fan, J. / Tang, W. / Wang, D. / Ge, H. / Rong, H. / Teng, M. / Niu, L. / Liu, Q. / Hao, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fe5.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fe5.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/3fe5 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/3fe5 | HTTPS FTP |
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-Related structure data
Related structure data | 2qnkS S: Starting model for refinement |
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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: 32448.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: Q0VCA8, 3-hydroxyanthranilate 3,4-dioxygenase |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 40% (NH4)2SO4, Tris-HCl, 40mM MgCl2, 3% MPD, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 1996 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→35.07 Å / Num. all: 8486 / Num. obs: 8486 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.51→2.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.041 / Mean I/σ(I) obs: 3.1 / Num. unique all: 183 / % possible all: 60 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QNK Resolution: 2.51→35.07 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.87 / SU B: 11.378 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.351 / 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: 20.254 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→35.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.515→2.58 Å / Total num. of bins used: 20
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