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Yorodumi- PDB-5xfw: Crystal structures of FMN-free form of dihydroorotate dehydrogena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xfw | ||||||
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Title | Crystal structures of FMN-free form of dihydroorotate dehydrogenase from Trypanosoma brucei | ||||||
Components | Dihydroorotate dehydrogenase (fumarate) | ||||||
Keywords | OXIDOREDUCTASE / Neglected Tropical Diseases Flavin Enzyme Pyrimidine metabolism | ||||||
Function / homology | Function and homology information 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 | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kubota, T. / Tani, O. / Yamaguchi, T. / Namatame, I. / Sakashita, H. / Furukawa, K. / Yamasaki, K. | ||||||
Citation | Journal: FEBS Open Bio / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xfw.cif.gz | 263.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xfw.ent.gz | 212.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/5xfw ftp://data.pdbj.org/pub/pdb/validation_reports/xf/5xfw | HTTPS FTP |
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-Related structure data
Related structure data | 5xfvC 2b4gS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote) Strain: 927/4 GUTat10.1 / Gene: Tb927.5.3830 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q57U83, dihydroorotate dehydrogenase (fumarate) #2: Chemical | ChemComp-MLI / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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