+Open data
-Basic information
Entry | Database: PDB / ID: 4yra | ||||||
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Title | mouse TDH in the apo form | ||||||
Components | L-threonine 3-dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / L-threonine 3-dehydrogenase | ||||||
Function / homology | Function and homology information L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / L-threonine catabolic process to glycine / threonine catabolic process / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | He, C. / Li, F. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Structural insights on mouse l-threonine dehydrogenase: A regulatory role of Arg180 in catalysis Authors: He, C. / Huang, X. / Liu, Y. / Li, F. / Yang, Y. / Tao, H. / Han, C. / Zhao, C. / Xiao, Y. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yra.cif.gz | 670.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yra.ent.gz | 555.9 KB | Display | PDB format |
PDBx/mmJSON format | 4yra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/4yra ftp://data.pdbj.org/pub/pdb/validation_reports/yr/4yra | HTTPS FTP |
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-Related structure data
Related structure data | 4yr9SC 4yrbC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 36734.891 Da / Num. of mol.: 12 / Fragment: UNP residues 47-373 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdh / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K3F7, L-threonine 3-dehydrogenase #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: 2.72 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Sodium HEPES, 10%(w/v) PEG 4000, 10%(v/v) 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→50 Å / Num. obs: 127736 / % possible obs: 93.9 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.051 / Rrim(I) all: 0.081 / Χ2: 1.287 / Net I/av σ(I): 13.95 / Net I/σ(I): 10.3 / Num. measured all: 266100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YR9 Resolution: 2.65→44.35 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2634 / WRfactor Rwork: 0.2096 / FOM work R set: 0.7967 / SU B: 13.99 / SU ML: 0.286 / SU R Cruickshank DPI: 1.1627 / SU Rfree: 0.3645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.163 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.29 Å2 / Biso mean: 65.471 Å2 / Biso min: 30.95 Å2
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Refinement step | Cycle: final / Resolution: 2.65→44.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.649→2.718 Å / Total num. of bins used: 20
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