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Yorodumi- PDB-3aov: Crystal structure of Pyrococcus horikoshii kynurenine aminotransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aov | ||||||
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Title | Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PLP | ||||||
Components | Putative uncharacterized protein PH0207 | ||||||
Keywords | TRANSFERASE / Protein-PLP complex / Schiff-base linkage / Kynurenin aminotransferase / Cofactor complex / aminotransferase / PLP binding / Transamination | ||||||
Function / homology | Function and homology information alpha-amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Okada, K. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: To be Published Title: Characterization of kynurenine aminotransferase from hyperthermophilic archaeon: enzymatic activity for conversion to kynurenic acid is allosterically regulated by alpha-ketoglutaric acid ...Title: Characterization of kynurenine aminotransferase from hyperthermophilic archaeon: enzymatic activity for conversion to kynurenic acid is allosterically regulated by alpha-ketoglutaric acid cooperatively with kynurenine Authors: Okada, K. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aov.cif.gz | 186.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aov.ent.gz | 145.9 KB | Display | PDB format |
PDBx/mmJSON format | 3aov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aov_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 3aov_full_validation.pdf.gz | 478.5 KB | Display | |
Data in XML | 3aov_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 3aov_validation.cif.gz | 54.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/3aov ftp://data.pdbj.org/pub/pdb/validation_reports/ao/3aov | HTTPS FTP |
-Related structure data
Related structure data | 3aowC 3athC 1x0mS 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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Unit cell |
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-Components
#1: Protein | Mass: 51162.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0207 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: O57946, kynurenine-oxoglutarate transaminase #2: Chemical | #3: 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: 2.03 Å3/Da / Density % sol: 39.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M magnesium chloride hexahydrate, 0.1M HEPES sodium pH7.5, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2010 / Details: mirrors |
Radiation | Monochromator: Rh mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 86393 / % possible obs: 99.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.071 / Rsym value: 0.063 / Net I/σ(I): 31.6 |
Reflection shell | Highest resolution: 1.72 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.75 / Num. unique all: 4357 / Rsym value: 0.415 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X0M Resolution: 1.72→26.84 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.569 / SU ML: 0.084 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.12 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.879 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→26.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.719→1.764 Å / Total num. of bins used: 20
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