[English] 日本語
Yorodumi- PDB-3ah3: Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase creat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ah3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution | ||||||
Components | Homoisocitrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 3-isopropylmalate dehydrogenase / homoisocitrate dehydrogenase / directed evolution | ||||||
Function / homology | Function and homology information isocitrate-homoisocitrate dehydrogenase / homoisocitrate dehydrogenase activity / isocitrate dehydrogenase (NAD+) activity / lysine biosynthetic process via aminoadipic acid / isocitrate metabolic process / tricarboxylic acid cycle / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Tomita, T. / Suzuki, Y. / Kuzuyama, T. / Nishiyama, M. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution Authors: Suzuki, Y. / Asada, K. / Miyazaki, J. / Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ah3.cif.gz | 433.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ah3.ent.gz | 349 KB | Display | PDB format |
PDBx/mmJSON format | 3ah3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3ah3 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3ah3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1x0lS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35862.332 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: LR5-1 / Plasmid: pET-LR5-1, pET 26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILCodonPlus / References: UniProt: Q72IW9, homoisocitrate dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | THESE MUTATIONS HAVE BEEN INTRODUCED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.24 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 3350, 27% MPD, 100mM Imidazole (pH 6.5), 200mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 67714 / Num. obs: 67714 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.346 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X0L Resolution: 2.4→49.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.611 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.166 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.396→2.458 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|