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Yorodumi- PDB-3ajr: Crystal structure of L-3-Hydroxynorvaline bound L-Threonine dehyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ajr | ||||||
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Title | Crystal structure of L-3-Hydroxynorvaline bound L-Threonine dehydrogenase (Y137F) from Hyperthermophilic Archaeon Thermoplasma volcanium | ||||||
Components | NDP-sugar epimerase | ||||||
Keywords | OXIDOREDUCTASE / L-threonine dehydrogenase / Thermoplasma volcanium / L-3-Hydroxynorvaline | ||||||
Function / homology | Function and homology information L-threonine 3-dehydrogenase activity / threonine catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Thermoplasma volcanium (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Yoneda, K. / Sakuraba, H. / Ohshima, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal Structure of Binary and Ternary Complexes of Archaeal UDP-galactose 4-Epimerase-like L-Threonine Dehydrogenase from Thermoplasma volcanium. Authors: Yoneda, K. / Sakuraba, H. / Araki, T. / Ohshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ajr.cif.gz | 141.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ajr.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ajr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ajr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3ajr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ajr_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 3ajr_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/3ajr ftp://data.pdbj.org/pub/pdb/validation_reports/aj/3ajr | HTTPS FTP |
-Related structure data
Related structure data | 3a1nC 3a4vC 3a9wSC C: citing same article (ref.) 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35871.891 Da / Num. of mol.: 2 / Mutation: Y137F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma volcanium (archaea) / Strain: GSS1 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q97BK3, L-threonine 3-dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.02 Å3/Da / Density % sol: 39.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 50% MPD, 0.1M SODIUM CACODYLATE(PH6.4), 5% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→82.761 Å / Num. obs: 54564 / % possible obs: 97.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.048 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 4.9 % / Rsym value: 0.146 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A9W Resolution: 1.77→33.914 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2647913.01 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.0396 Å2 / ksol: 0.377828 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.44 Å2 / Biso mean: 24.8 Å2 / Biso min: 11.46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.77→33.914 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.88 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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