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Yorodumi- PDB-3e2f: Crystal structure of mouse kynurenine aminotransferase III, PLP-b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e2f | ||||||
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Title | Crystal structure of mouse kynurenine aminotransferase III, PLP-bound form | ||||||
Components | Kynurenine-oxoglutarate transaminase 3Kynurenine—oxoglutarate transaminase | ||||||
Keywords | TRANSFERASE / LYASE / alpha beta protein / PLP dependent protein / Aminotransferase / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / cysteine-S-conjugate beta-lyase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process ...cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / cysteine-S-conjugate beta-lyase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process / biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Han, Q. / Robinson, R. / Cai, T. / Tagle, D.A. / Li, J. | ||||||
Citation | Journal: Mol. Cell. Biol. / Year: 2018 Title: Correction for Han et al., "Biochemical and Structural Properties of Mouse Kynurenine Aminotransferase III". Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J. #1: Journal: Mol.Cell.Biol. / Year: 2009 Title: Biochemical and structural properties of mouse kynurenine aminotransferase III. Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e2f.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e2f.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 3e2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/3e2f ftp://data.pdbj.org/pub/pdb/validation_reports/e2/3e2f | HTTPS FTP |
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-Related structure data
Related structure data | 3e2yC 3e2zC 2zjgS C: citing same article (ref.) 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: 46453.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ccbl2, Kat3 / Plasmid: pBlueBac4.5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q71RI9, kynurenine-oxoglutarate transaminase, cysteine-S-conjugate beta-lyase #2: Chemical | ChemComp-GOL / #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: 2.39 Å3/Da / Density % sol: 48.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21% PEG 400, 150 mM CaCl2, 10% Glycerol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→30 Å / Num. all: 32023 / Num. obs: 29301 / % possible obs: 91.1 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.15 |
Reflection shell | Resolution: 2.59→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZJG Resolution: 2.59→29.21 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / ESU R: 1.694 / ESU R Free: 0.331 / 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: 30.531 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→29.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.66 Å / Total num. of bins used: 20
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