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Yorodumi- PDB-5eun: The Crystal Structure of Human Kynurenine Aminotransferase II, PL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eun | ||||||
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Title | The Crystal Structure of Human Kynurenine Aminotransferase II, PLP-bound form, at 1.83 A | ||||||
Components | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | ||||||
Keywords | TRANSFERASE / Kynurenine Aminotransferase II / LLP | ||||||
Function / homology | Function and homology information glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / alpha-amino acid metabolic process / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / 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 / alpha-amino acid metabolic process / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / 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: 1.825 Å | ||||||
Authors | Nematollahi, A. / Sun, G. / Kwan, A. / Jeffries, C.M. / Harrop, S.J. / Hanrahan, J.R. / Nadvi, N.A. / Church, W.B. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2016 Title: Structure of the PLP-Form of the Human Kynurenine Aminotransferase II in a Novel Spacegroup at 1.83 angstrom Resolution. Authors: Nematollahi, A. / Sun, G. / Harrop, S.J. / Hanrahan, J.R. / Church, W.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eun.cif.gz | 262.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eun.ent.gz | 224.2 KB | Display | PDB format |
PDBx/mmJSON format | 5eun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5eun ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5eun | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47628.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AADAT, KAT2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: Q8N5Z0, 2-aminoadipate transaminase, kynurenine-oxoglutarate transaminase |
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#2: 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: 2.4 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein (1 uL) at a concentration of 7 mg/mL were mixed with an equal volume of a reservoir solution containing 200 mM NaCl, 0.1M NaCitrate pH 5.6, 24% PEG4K and equilibrated against 1 mL of ...Details: Protein (1 uL) at a concentration of 7 mg/mL were mixed with an equal volume of a reservoir solution containing 200 mM NaCl, 0.1M NaCitrate pH 5.6, 24% PEG4K and equilibrated against 1 mL of a reservoir solution at 293 K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.825→45.86 Å / Num. obs: 40742 / % possible obs: 98.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.83→1.89 Å / Redundancy: 2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 2.9 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.825→40.462 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.825→40.462 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.9102 Å / Origin y: 16.761 Å / Origin z: 13.6756 Å
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Refinement TLS group | Selection details: all |