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Yorodumi- PDB-3b46: Crystal Structure of Bna3p, a Putative Kynurenine Aminotransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b46 | ||||||
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Title | Crystal Structure of Bna3p, a Putative Kynurenine Aminotransferase from Saccharomyces cerevisiae | ||||||
Components | Aminotransferase BNA3 | ||||||
Keywords | TRANSFERASE / kynurenine aminotransferase / LLP / PLP / Cytoplasm / Mitochondrion / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information Phenylalanine metabolism / Glutamate and glutamine metabolism / Tryptophan catabolism / 2-aminoadipate transaminase activity / L-kynurenine catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenic acid biosynthetic process / pyridoxal phosphate binding / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wogulis, M. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Identification of Formyl Kynurenine Formamidase and Kynurenine Aminotransferase from Saccharomyces cerevisiae Using Crystallographic, Bioinformatic and Biochemical Evidence. Authors: Wogulis, M. / Chew, E.R. / Donohoue, P.D. / Wilson, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b46.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b46.ent.gz | 144.1 KB | Display | PDB format |
PDBx/mmJSON format | 3b46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b46_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 3b46_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 3b46_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 3b46_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/3b46 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b46 | HTTPS FTP |
-Related structure data
Related structure data | 1w7lS 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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Details | The asymmetric unit contains one biological assembly. |
-Components
#1: Protein | Mass: 50630.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BNA3 / Plasmid: pTYB12 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P47039, Transferases; Transferring nitrogenous groups; Transaminases #2: 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: 2.11 Å3/Da / Density % sol: 41.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10 mM Tris, 50 mM NaCl, 14 mM mercaptoethanol, 0.025 mM PLP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97944 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2006 Details: Double-crystal monochromator, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing |
Radiation | Monochromator: Double crystal, paralell / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 60609 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 36.9 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.7 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1W7L Resolution: 2→28.8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1708275.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.5103 Å2 / ksol: 0.368472 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→28.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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