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Yorodumi- PDB-4ydr: Crystal structure of oxidized homoserine dehydrogenase of Sulfolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ydr | ||||||
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Title | Crystal structure of oxidized homoserine dehydrogenase of Sulfolobus tokodaii | ||||||
Components | Homoserine dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Oxidized form | ||||||
Function / homology | Function and homology information homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / NADP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Goto, M. / Yoshimune, K. / Kaneko, R. | ||||||
Citation | Journal: Biochem Biophys Rep / Year: 2015 Title: Structural insight into activation of homoserine dehydrogenase from the archaeonSulfolobus tokodaiivia reduction. Authors: Tomonaga, Y. / Kaneko, R. / Goto, M. / Ohshima, T. / Yoshimune, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ydr.cif.gz | 128.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ydr.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ydr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/4ydr ftp://data.pdbj.org/pub/pdb/validation_reports/yd/4ydr | HTTPS FTP |
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-Related 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: 33411.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea) Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: hom, STK_15190 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F9VNG5, homoserine dehydrogenase #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.11 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, magnesium chloride, PEG 400, DMSO / PH range: 6.5-9.0 |
-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 270 / Detector: CCD / Date: Nov 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 74576 / % possible obs: 99.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 38.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 7.2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.724 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 24.553 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→28.5 Å
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Refine LS restraints |
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