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- PDB-6hfk: Human dihydroorotase mutant F1563L co-crystallized with carbamoyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hfk | ||||||
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Title | Human dihydroorotase mutant F1563L co-crystallized with carbamoyl aspartate at pH 6.5 | ||||||
![]() | CAD protein | ||||||
![]() | BIOSYNTHETIC PROTEIN / de novo pyrimidine biosynthesis / CAD / TIM-barrel / carboxylated lysine | ||||||
Function / homology | ![]() aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase ...aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase / aspartate carbamoyltransferase activity / dihydroorotase activity / Pyrimidine biosynthesis / glutaminase activity / UTP biosynthetic process / UDP biosynthetic process / response to caffeine / response to testosterone / glutamine metabolic process / response to amine / response to starvation / 'de novo' UMP biosynthetic process / animal organ regeneration / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to epidermal growth factor stimulus / lactation / xenobiotic metabolic process / liver development / cell projection / female pregnancy / peptidyl-threonine phosphorylation / response to insulin / terminal bouton / nuclear matrix / heart development / protein autophosphorylation / protein kinase activity / neuronal cell body / enzyme binding / protein-containing complex / zinc ion binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramon-Maiques, S. / Grande Garcia, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD. Authors: Del Cano-Ochoa, F. / Grande-Garcia, A. / Reverte-Lopez, M. / D'Abramo, M. / Ramon-Maiques, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.7 KB | Display | ![]() |
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PDB format | ![]() | 194.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.3 KB | Display | ![]() |
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Full document | ![]() | 469.1 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hfdC ![]() 6hfeC ![]() 6hffC ![]() 6hfhC ![]() 6hfiC ![]() 6hfjC ![]() 6hflC ![]() 6hfnC ![]() 6hfpC ![]() 6hfqC ![]() 6hfrC ![]() 6hfsC ![]() 6hfuC ![]() 6hg1C ![]() 6hg2C ![]() 6hg3C ![]() 4c6iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 42882.000 Da / Num. of mol.: 1 / Mutation: F1563L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), aspartate carbamoyltransferase, dihydroorotase | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-DOR / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein at 2-3 mg/ml in 20 mM Tris pH 8, 0.15 M NaCl, 0.02 mM zinc sulfate, 0.2 mM TCEP with 4 mM carbamoyl asparate. Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45914405408→44.4672218597 Å / Num. obs: 69136 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 19.0718984219 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.053 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.45914405408→1.51 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6795 / CC1/2: 0.881 / Rrim(I) all: 0.687 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4C6I Resolution: 1.45914405408→44.4672218597 Å / SU ML: 0.0982519831041 / Cross valid method: FREE R-VALUE / σ(F): 1.34747701184 / Phase error: 10.8490166872
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.0565433375 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45914405408→44.4672218597 Å
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Refine LS restraints |
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LS refinement shell |
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