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- PDB-3tjx: Crystal Structure of Leishmania major dihydroorotate dehydrogenas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tjx | ||||||
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Title | Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant H174A | ||||||
![]() | Dihydroorotate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / dihydroorotate dehydrogenase / pyrd / DHODH / LmDHODH / mutation H174A / Leishmania major | ||||||
Function / homology | ![]() dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Souza, A.L. / Nonato, M.C. / Pinheiro, M.P. | ||||||
![]() | ![]() Title: Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant H174A Authors: de Souza, A.L. / Nonato, M.C. / Pinheiro, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.5 KB | Display | ![]() |
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PDB format | ![]() | 116.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 45.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gyeS ![]() 3snq ![]() 3snu 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
#1: Protein | Mass: 38178.574 Da / Num. of mol.: 2 / Mutation: H174A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M sodium citrate tribasic dihydrate, 1.3M lithium sulfate, 0.30M amonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2010 |
Radiation | Monochromator: Si Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→24.52 Å / Num. obs: 100794 / % possible obs: 99.9 % / Observed criterion σ(I): 2.5 / Redundancy: 4.5 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.64→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.7 / Num. unique all: 14685 / Rsym value: 0.309 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GYE Resolution: 1.64→24.52 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / σ(I): 2.4 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 20.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→24.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.637→1.679 Å / Total num. of bins used: 20
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