[English] 日本語
Yorodumi- PDB-4xq6: CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENSE from MYCOBACTERI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xq6 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENSE from MYCOBACTERIUM TUBERCULOSIS | ||||||
Components | Dihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE / DIHYDROOROTATE DEHYDROGENSE | ||||||
Function / homology | Function and homology information pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Ra (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Kishor, C. / Addlagatta, A. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Dihydroorotate Dehydrogenase form Mycobacterium Tuberculosis Authors: Kishor, C. / Addlagatta, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xq6.cif.gz | 140.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xq6.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xq6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4xq6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4xq6_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 4xq6_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/4xq6 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/4xq6 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36465.406 Da / Num. of mol.: 2 / Fragment: UNP residues 31-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria) Strain: H37Ra / Gene: pyrD, MRA_2153 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: A5U4G5, UniProt: P9WHL1*PLUS, dihydroorotate dehydrogenase (quinone) #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 22-27% PEG 3350, 0.1M Bis-Tris pH 5.0, 0.2M Mgcl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 13, 2014 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→27 Å / Num. obs: 39530 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 11.64 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→23.47 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.257 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.179 / 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: 28.673 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→23.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|