[English] 日本語
Yorodumi- PDB-4y1p: Crystal structure of 3-isopropylmalate dehydrogenase (Saci_0600) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y1p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of 3-isopropylmalate dehydrogenase (Saci_0600) from Sulfolobus acidocaldarius complex with 3-isopropylmalate and Mg2+ | ||||||
Components | 3-isopropylmalate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / beta-decarboxylating dehyrogenase / 3-isopropylmalate dehydrogenase / Sulfolobus acidocaldarius / Closed form | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus acidocaldarius DSM 639 (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Takahashi, K. / Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Extremophiles / Year: 2016 Title: Characterization of two beta-decarboxylating dehydrogenases from Sulfolobus acidocaldarius Authors: Takahashi, K. / Nakanishi, F. / Tomita, T. / Akiyama, N. / Lassak, K. / Albers, S.V. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4y1p.cif.gz | 144 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4y1p.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 4y1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y1p_validation.pdf.gz | 475.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4y1p_full_validation.pdf.gz | 482 KB | Display | |
Data in XML | 4y1p_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 4y1p_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/4y1p ftp://data.pdbj.org/pub/pdb/validation_reports/y1/4y1p | HTTPS FTP |
-Related structure data
Related structure data | 1a05S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36477.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic) Strain: DSM 639 / Gene: leuB, Saci_0600 / Plasmid: pET-Saci_0600 / Production host: Escherichia coli (E. coli) References: UniProt: Q4JB37, 3-isopropylmalate dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.0 M Ammonium sulfate, 0.1 M Cacodylate (pH6.5), 0.2 M NaCl PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 35126 / % possible obs: 99.7 % / Redundancy: 7.3 % / Net I/σ(I): 17.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A05 Resolution: 2.2→33.51 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.974 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.225 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.169 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→33.51 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|