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Yorodumi- PDB-4by3: Crystal structure of the dihydroorotase domain of human CAD in ap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4by3 | |||||||||
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Title | Crystal structure of the dihydroorotase domain of human CAD in apo- form obtained recombinantly from E. coli. | |||||||||
Components | DIHYDROOROTASE | |||||||||
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: 1.73 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 | 4by3.cif.gz | 239.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4by3.ent.gz | 194.7 KB | Display | PDB format |
PDBx/mmJSON format | 4by3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4by3_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 4by3_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 4by3_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 4by3_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/4by3 ftp://data.pdbj.org/pub/pdb/validation_reports/by/4by3 | HTTPS FTP |
-Related structure data
Related structure data | 4c6bC 4c6cC 4c6dC 4c6eC 4c6fC 4c6iC 4c6jC 4c6kC 4c6lC 4c6mC 4c6nC 4c6oC 4c6pC 4c6qC 2z00S S: Starting model for refinement C: citing same article (ref.) |
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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: 42916.020 Da / Num. of mol.: 1 / Fragment: RESIDUES 1456-1846 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPIN-M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P27708, EC: 3.4.2.3 | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FMT / #4: 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: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→19.9 Å / Num. obs: 42366 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 20.05 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.73→1.77 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.1 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z00 Resolution: 1.73→19.856 Å / SU ML: 0.09 / σ(F): 1.99 / Phase error: 10.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→19.856 Å
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Refine LS restraints |
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LS refinement shell |
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