[English] 日本語
Yorodumi- PDB-1v5b: The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v5b | ||||||
---|---|---|---|---|---|---|---|
Title | The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans | ||||||
Components | 3-isopropylmalate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 3-isopropylmalate dehydrogenase / IPMDH / mutant / S225A/E251L / Bacillus coagulans / homo dimer / X-ray analysis | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / amino acid biosynthetic process / NAD binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus coagulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Fujita, K. / Minami, H. / Suzuki, K. / Tsunoda, M. / Sekiguchi, T. / Mizui, R. / Tsuzaki, S. / Nakamura, S. / Takenaka, A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of a highly thermo-stabilized mutant of 3-isopropylmalate dehydrogenase from Bacillus coagulans: An evaluation of local packing density in the hydrophobic core Authors: Fujita, K. / Tsuchiya, D. / Adachi, W. / Suzuki, K. / Tsunoda, M. / Minami, H. / Sekiguchi, T. / Kobayashi, N. / Mizui, R. / Tsuzaki, S. / Nakamura, S. / Takenaka, A. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The asymmetric unit contains four homo-dimeric enzymes, alpha composed of two subunits A and B, beta C and D, gamma E and F and delta G and H. To form a tetrameric cluster as described in the paper, alpha and beta should be converted by a symmetry code (iii) and gamma should be converted by a symmetry code (iv). Symmetry code (iii):1-x, y-1/2, 1/2-z Symmetry code (iv):x+1/2, 3/2-y, 1-z In addition, the cluster should be converted by 1-x,1/2-y,z. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1v5b.cif.gz | 524.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1v5b.ent.gz | 435.1 KB | Display | PDB format |
PDBx/mmJSON format | 1v5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/1v5b ftp://data.pdbj.org/pub/pdb/validation_reports/v5/1v5b | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ayqS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39723.438 Da / Num. of mol.: 8 / Mutation: S225A, E251L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus coagulans (bacteria) / Plasmid: pUCBCO, pUC118 / Production host: Escherichia coli (E. coli) References: UniProt: P12010, 3-isopropylmalate dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.68 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: OXFORD PX210 / Detector: CCD / Date: May 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→44.45 Å / Num. all: 136367 / Num. obs: 74349 / % possible obs: 90.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.95→3.06 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.4 / % possible all: 92.7 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AYQ Resolution: 2.95→44.45 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→44.45 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.95→2.99 Å
|