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Yorodumi- PDB-2r2n: The crystal structure of human kynurenine aminotransferase II in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r2n | ||||||
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Title | The crystal structure of human kynurenine aminotransferase II in complex with kynurenine | ||||||
Components | Kynurenine/alpha-aminoadipate aminotransferase mitochondrial | ||||||
Keywords | TRANSFERASE / alpha & beta protein / PLP-dependent transferase / Aminotransferase / Mitochondrion / Multifunctional enzyme / Pyridoxal phosphate / Transit peptide | ||||||
Function / homology | Function and homology information glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / alpha-amino acid metabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine ...glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / alpha-amino acid metabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / Lysine catabolism / glutamate metabolic process / 2-oxoglutarate metabolic process / Tryptophan catabolism / biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Han, Q. / Robinson, H. / Li, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal structure of human kynurenine aminotransferase II. Authors: Han, Q. / Robinson, H. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r2n.cif.gz | 368 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r2n.ent.gz | 300.1 KB | Display | PDB format |
PDBx/mmJSON format | 2r2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/2r2n ftp://data.pdbj.org/pub/pdb/validation_reports/r2/2r2n | HTTPS FTP |
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-Related structure data
Related structure data | 2qlrSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47400.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AADAT, KAT2 / Plasmid: PTYB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q8N5Z0, kynurenine-oxoglutarate transaminase, 2-aminoadipate transaminase #2: Chemical | ChemComp-PMP / #3: Chemical | ChemComp-KYN / ( #4: Chemical | ChemComp-GOL / #5: 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: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Hepes, 15% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 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, 2007 |
Radiation | Monochromator: SI 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 132070 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.092 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.373 / % possible all: 62.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2qlr Resolution: 1.95→26.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.161 / 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: 29.617 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→26.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.949→1.999 Å / Total num. of bins used: 20
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