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Yorodumi- PDB-4c6n: Crystal structure of the dihydroorotase domain of human CAD E1637... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c6n | ||||||
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Title | Crystal structure of the dihydroorotase domain of human CAD E1637T mutant bound to substrate at pH 6.0 | ||||||
Components | CAD PROTEIN | ||||||
Keywords | HYDROLASE / DE NOVO PYRIMIDINE BIOSYNTHESIS / AMIDOHYDROLASE SUPERFAMILY / METALLOENZYME / ZINC BINDING / HISTIDINATE ANION | ||||||
Function / homology | Function and homology information 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 / UDP biosynthetic process / UTP biosynthetic process / response to caffeine / response to testosterone / glutamine metabolic process / response to starvation / response to amine / cellular response to epidermal growth factor stimulus / 'de novo' UMP biosynthetic process / animal organ regeneration / 'de novo' pyrimidine nucleobase biosynthetic process / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å | ||||||
Authors | Ramon-Maiques, S. / Lallous, N. / Grande-Garcia, A. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structure, Functional Characterization and Evolution of the Dihydroorotase Domain of Human Cad. Authors: Grande-Garcia, A. / Lallous, N. / Diaz-Tejada, C. / Ramon-Maiques, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c6n.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c6n.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 4c6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c6n_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 4c6n_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 4c6n_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 4c6n_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/4c6n ftp://data.pdbj.org/pub/pdb/validation_reports/c6/4c6n | HTTPS FTP |
-Related structure data
Related structure data | 4by3C 4c6bC 4c6cSC 4c6dC 4c6eC 4c6fC 4c6iC 4c6jC 4c6kC 4c6lC 4c6mC 4c6oC 4c6pC 4c6qC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42888.008 Da / Num. of mol.: 1 / Fragment: RESIDUES 1456-1846 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPIN-M / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P27708, dihydroorotase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NCD / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 6 / Details: pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.4 Å / Num. obs: 31728 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 21.05 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 6.1 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C6C Resolution: 1.899→48.399 Å / SU ML: 0.11 / σ(F): 2 / Phase error: 16.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.899→48.399 Å
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Refine LS restraints |
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LS refinement shell |
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