[English] 日本語
Yorodumi- PDB-1wal: 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) MUTANT (M219A)FROM THERMU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wal | ||||||
---|---|---|---|---|---|---|---|
Title | 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) MUTANT (M219A)FROM THERMUS THERMOPHILUS | ||||||
Components | PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE / LEUCINE BIOSYNTHESIS / NAD-DEPENDANT ENZYME | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Wallon, G. / Kryger, G. / Lovett, S.T. / Oshima, T. / Ringe, D. / Petsko, G.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus. Authors: Wallon, G. / Kryger, G. / Lovett, S.T. / Oshima, T. / Ringe, D. / Petsko, G.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wal.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wal.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/1wal ftp://data.pdbj.org/pub/pdb/validation_reports/wa/1wal | HTTPS FTP |
---|
-Related structure data
Related structure data | 1cm7C 1cnzC 1ipdS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36694.926 Da / Num. of mol.: 1 / Mutation: M219A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: LEUB / Plasmid: PET21C LEUB / Species (production host): Escherichia coli / Gene (production host): LEUB / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61495 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 67.82 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.6 / Details: 6 MG/ML PROTEIN IN 1.4 M AMMONIUM SULFATE, pH 7.6 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→30 Å / Num. obs: 54255 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.055 |
Reflection | *PLUS Num. obs: 22587 / Num. measured all: 54255 / Rmerge(I) obs: 0.055 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IPD Resolution: 2.27→6 Å / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.01 |