[English] 日本語
Yorodumi- PDB-6jx2: Crystal structure of Ketol-acid reductoisomerase from Corynebacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jx2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Ketol-acid reductoisomerase from Corynebacterium glutamicum | ||||||
Components | Ketol-acid reductoisomerase (NADP(+)) | ||||||
Keywords | OXIDOREDUCTASE / Ketol-acid reductoisomerase | ||||||
Function / homology | Function and homology information 2-dehydropantoate 2-reductase activity / ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lee, D. / Hong, J. / Kim, K.-J. | ||||||
Citation | Journal: J.Agric.Food Chem. / Year: 2019 Title: Crystal Structure and Biochemical Characterization of Ketol-Acid Reductoisomerase fromCorynebacterium glutamicum. Authors: Lee, D. / Hong, J. / Kim, K.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jx2.cif.gz | 255.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jx2.ent.gz | 205 KB | Display | PDB format |
PDBx/mmJSON format | 6jx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/6jx2 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/6jx2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ypoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37021.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Strain: ATCC 13032 / Gene: ilvC, Cgl1273, cg1437 / Plasmid: pET30a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): T1R(DE3) References: UniProt: Q57179, ketol-acid reductoisomerase (NADP+) #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.54 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25 % (w/v) polyethylene glycol (PEG) 3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M Magnesium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 6, 2016 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→78.91 Å / Num. obs: 37218 / % possible obs: 98.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.6→2.64 Å / Num. unique obs: 37218 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YPO Resolution: 2.6→78.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.899 / SU B: 14.245 / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.378 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.24 Å2 / Biso mean: 54.779 Å2 / Biso min: 24.02 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→78.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|