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Yorodumi- PDB-1g2u: THE STRUCTURE OF THE MUTANT, A172V, OF 3-ISOPROPYLMALATE DEHYDROG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2u | ||||||
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Title | THE STRUCTURE OF THE MUTANT, A172V, OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 : ITS THERMOSTABILITY AND STRUCTURE. | ||||||
Components | 3-ISOPROPYLMALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / BETA-BARREL / NAD BINDING | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Qu, C. / Akanuma, S. / Tanaka, N. / Moriyama, H. / Oshima, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Design, X-ray crystallography, molecular modelling and thermal stability studies of mutant enzymes at site 172 of 3-isopropylmalate dehydrogenase from Thermus thermophilus. Authors: Qu, C. / Akanuma, S. / Tanaka, N. / Moriyama, H. / Oshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2u.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2u.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 1g2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2u ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2u | HTTPS FTP |
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-Related structure data
Related structure data | 1gc8C 1gc9C 1ost 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: 36853.211 Da / Num. of mol.: 1 / Mutation: A172V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: LEU B / Plasmid: PULT-119 / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.81 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.66M ammonium sulfate, 10mM phosphate buffer, 28mg/ml protein , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Sakurai, M., (1992) J.Biochem., 112, 173. / PH range low: 8.5 / PH range high: 6 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 12, 1998 / Details: mirror and beta-filter |
Radiation | Monochromator: Beta-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 29.8 Å2 |
Reflection | *PLUS Highest resolution: 2.1 Å / Rmerge(I) obs: 89.4 / Rmerge F obs: 0.0583 |
-Processing
Software |
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Refinement | Resolution: 2.1→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3474165.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 31 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection obs: 21122 / Rfactor obs: 0.185 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.304 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.269 |