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- PDB-5xfw: Crystal structures of FMN-free form of dihydroorotate dehydrogena... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xfw | ||||||
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Title | Crystal structures of FMN-free form of dihydroorotate dehydrogenase from Trypanosoma brucei | ||||||
![]() | Dihydroorotate dehydrogenase (fumarate) | ||||||
![]() | OXIDOREDUCTASE / Neglected Tropical Diseases Flavin Enzyme Pyrimidine metabolism | ||||||
Function / homology | ![]() dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / glycosome / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kubota, T. / Tani, O. / Yamaguchi, T. / Namatame, I. / Sakashita, H. / Furukawa, K. / Yamasaki, K. | ||||||
![]() | ![]() Title: Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase fromTrypanosoma brucei. Authors: Kubota, T. / Tani, O. / Yamaguchi, T. / Namatame, I. / Sakashita, H. / Furukawa, K. / Yamasaki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263.5 KB | Display | ![]() |
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PDB format | ![]() | 212.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.7 KB | Display | ![]() |
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Full document | ![]() | 471.7 KB | Display | |
Data in XML | ![]() | 51.9 KB | Display | |
Data in CIF | ![]() | 75 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xfvC ![]() 2b4gS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36463.898 Da / Num. of mol.: 4 / Mutation: A115V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb927.5.3830 / Production host: ![]() ![]() References: UniProt: Q57U83, dihydroorotate dehydrogenase (fumarate) #2: Chemical | ChemComp-MLI / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: Parallelepiped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Sodium Citrate buffer, 1.5-2.5 M Sodium Malonate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 180934 / % possible obs: 99.4 % / Redundancy: 13.3 % / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.5 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2B4G Resolution: 1.6→36.95 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.791 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.679 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→36.95 Å
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Refine LS restraints |
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