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Yorodumi- PDB-1gc8: THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gc8 | ||||||
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Title | THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TO PHE | ||||||
Components | 3-ISOPROPYLMALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / IPMDH / IMDH / Thermostability / dehydrogenation / decarboxylation | ||||||
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: 2.5 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 | 1gc8.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gc8.ent.gz | 109.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gc8 ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gc8 | 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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Details | The biological assembly is a dimer constructed from chain A and a symmetry partner generated by the non-crystallographic symmetry. |
-Components
#1: Protein | Mass: 36901.254 Da / Num. of mol.: 2 / Mutation: A172F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: LEUB / Plasmid: JA221 / Production host: Escherichia coli (E. coli) References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 46.6 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: PEG4000, potassium phosphate, sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
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: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 13, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 20952 / % possible obs: 89.4 % / Observed criterion σ(F): 2 / Redundancy: 3.15 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 2.5→2.75 Å / Rmerge(I) obs: 0.184 / Num. unique all: 5224 |
Reflection | *PLUS % possible obs: 92.8 % / Rmerge(I) obs: 0.0558 |
-Processing
Software |
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Refinement | Resolution: 2.5→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3855261.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 20506 / % reflection Rfree: 9.8 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.297 / Rfactor Rwork: 0.253 |