+Open data
-Basic information
Entry | Database: PDB / ID: 5efs | ||||||
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Title | The crystal structure of human kynurenine aminotransferase II | ||||||
Components | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | ||||||
Keywords | TRANSFERASE / Kynurenine Aminotransferase II | ||||||
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: 1.82503 Å | ||||||
Authors | Nematollahi, A. / Sun, G. / Kwan, A. / Harrop, S.J. / Hanrahan, J.R. / Nadvi, N.A. / Church, W.B. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of human kynurenine aminotransferase II Authors: Nematollahi, A. / Sun, G. / Kwan, A. / Jeffries, C.M. / Harrop, S.J. / Hanrahan, J.R. / Nadvi, N.A. / 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 | 5efs.cif.gz | 263.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5efs.ent.gz | 217.1 KB | Display | PDB format |
PDBx/mmJSON format | 5efs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/5efs ftp://data.pdbj.org/pub/pdb/validation_reports/ef/5efs | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47400.434 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 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 200 mM NaCl, 0.1M NaCitrate pH 5.6, 24% PEG4K / PH range: 5.6 |
-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→45.82 Å / Num. obs: 40804 / % possible obs: 99.8 % / Redundancy: 14.3 % / Biso Wilson estimate: 17.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.029 / Net I/σ(I): 17 / Num. measured all: 585446 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82503→40.462 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.07 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 188.72 Å2 / Biso mean: 30.2793 Å2 / Biso min: 2.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.82503→40.462 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 16.7643 Å / Origin y: 26.9686 Å / Origin z: 29.4014 Å
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Refinement TLS group |
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