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Yorodumi- PDB-5vep: MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vep | ||||||
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Title | MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2F | ||||||
Components | Kynurenine--oxoglutarate transaminase 3 | ||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE III / MOUSE / RE-REFINEMENT | ||||||
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 | Wlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Porebski, P. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B. | ||||||
Citation | 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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Remark 0 | This entry reflects an alternative modeling of the original data in 3E2F, determined by Q.HAN,R. ...This entry reflects an alternative modeling of the original data in 3E2F, determined by Q.HAN,R.ROBINSON,T.CAI,D.A.TAGLE,J.LI | ||||||
Remark 200 | SEE THE ORIGINAL DATA, ENTRY 3E2F | ||||||
Remark 280 | SEE THE ORIGINAL DATA, ENTRY 3E2F |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vep.cif.gz | 175 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vep.ent.gz | 142.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vep_validation.pdf.gz | 477 KB | Display | wwPDB validaton report |
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Full document | 5vep_full_validation.pdf.gz | 493.1 KB | Display | |
Data in XML | 5vep_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 5vep_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/5vep ftp://data.pdbj.org/pub/pdb/validation_reports/ve/5vep | HTTPS FTP |
-Related structure data
Related structure data | 5vehC 5veqC 5verC 5vetC 5vf2C 5vf5C 5vgaC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#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: Kyat3, Ccbl2, Kat3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q71RI9, kynurenine-oxoglutarate transaminase, cysteine-S-conjugate beta-lyase, kynurenine-glyoxylate transaminase |
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-Non-polymers , 5 types, 176 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CA / #6: 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: 2.65 Å3/Da / Density % sol: 53.59 % |
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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 |
-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 |
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→29.21 Å / Num. obs: 29301 / % possible obs: 91.1 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→29.21 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.885 / SU B: 13.469 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.982 / ESU R Free: 0.356 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.57 Å2 / Biso mean: 36.919 Å2 / Biso min: 14.52 Å2
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Refinement step | Cycle: final / Resolution: 2.59→29.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.592→2.658 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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