[English] 日本語
Yorodumi- PDB-3tro: Crystal Structure of Leishmania major dihydroorotate dehydrogenas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tro | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant D171A | ||||||
Components | Dihydroorotate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / pyrd / DHODH / LmDHODH | ||||||
Function / homology | Function and homology information 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 | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | de Souza, A.L. / Pinheiro, M.P. / Nonato, M.C. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant D171A Authors: de Souza, A.L. / Pinheiro, M.P. / Nonato, M.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tro.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tro.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 3tro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tro_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tro_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3tro_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 3tro_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/3tro ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3tro | HTTPS FTP |
-Related structure data
Related structure data | 3gyeS 3snq 3snu S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38201.633 Da / Num. of mol.: 2 / Mutation: D171A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: DHODH, lmjf16.0530, LMJF_16_0530 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QEW7, EC: 1.3.3.1 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.63 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 1.3 M lithium sulfate, 0.30 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.437 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 14, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.437 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→20.82 Å / Num. obs: 68190 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 8 % / Biso Wilson estimate: 16.171 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.9 / Num. unique all: 9824 / Rsym value: 0.639 / % possible all: 98.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GYE Resolution: 1.86→19.61 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.978 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
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: 21.497 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→19.61 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.86→1.912 Å / Total num. of bins used: 20
|