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Yorodumi- PDB-3tq0: Crystal structure of Leishmania major dihydroorotate dehydrogenas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tq0 | |||||||||
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Title | Crystal structure of Leishmania major dihydroorotate dehydrogenase in complex with fumarate | |||||||||
Components | Dihydroorotate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
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: 1.9 Å | |||||||||
Authors | Cordeiro, A.T. / Feliciano, P.R. / Nonato, M.C. | |||||||||
Citation | Journal: Biochimie / Year: 2012 Title: Crystal structure of dihydroorotate dehydrogenase from Leishmania major. Authors: Cordeiro, A.T. / Feliciano, P.R. / Pinheiro, M.P. / Nonato, M.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tq0.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tq0.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 3tq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tq0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3tq0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3tq0_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3tq0_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/3tq0 ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tq0 | HTTPS FTP |
-Related structure data
Related structure data | 3gyeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37340.723 Da / Num. of mol.: 2 / Fragment: UNP residues 1-312 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 |
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-Non-polymers , 6 types, 399 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NI / | #6: Chemical | ChemComp-SO4 / #7: 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: 2.62 Å3/Da / Density % sol: 53.05 % |
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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, 0.3 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 24, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.427 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.812 Å / Num. all: 60971 / Num. obs: 60966 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.55 % / Rsym value: 0.079 / Net I/σ(I): 8.12 |
Reflection shell | Highest resolution: 1.9 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GYE Resolution: 1.9→29.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.061 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.599 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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