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Yorodumi- PDB-6hfh: Human dihydroorotase mutant F1563A co-crystallized with carbamoyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hfh | ||||||
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Title | Human dihydroorotase mutant F1563A co-crystallized with carbamoyl aspartate at pH 7.0 | ||||||
Components | CAD protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / de novo pyrimidine biosynthesis / CAD / TIM-barrel / carboxylated lysine | ||||||
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 / UDP biosynthetic process / glutaminase activity / UTP biosynthetic process / response to caffeine / response to testosterone / response to starvation / glutamine metabolic process / response to amine / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / animal organ regeneration / 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 / extracellular exosome / zinc ion binding / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44871265165 Å | ||||||
Authors | Ramon-Maiques, S. / Grande Garcia, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hfh.cif.gz | 289.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hfh.ent.gz | 194.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/6hfh ftp://data.pdbj.org/pub/pdb/validation_reports/hf/6hfh | HTTPS FTP |
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-Related structure data
Related structure data | 6hfdC 6hfeC 6hffC 6hfiC 6hfjC 6hfkC 6hflC 6hfnC 6hfpC 6hfqC 6hfrC 6hfsC 6hfuC 6hg1C 6hg2C 6hg3C 4c6iS 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: 42839.922 Da / Num. of mol.: 1 / Mutation: F1563A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Plasmid: pOPIN-M / Cell line (production host): HEK293-GnTI / Production host: Homo sapiens (human) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 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 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9795 Å |
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: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.44871265165→41.013 Å / Num. obs: 71360 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.9270057298 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.07 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6886 / CC1/2: 0.827 / Rrim(I) all: 0.758 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C6I Resolution: 1.44871265165→41.013 Å / SU ML: 0.117761145646 / Cross valid method: FREE R-VALUE / σ(F): 1.34366465596 / Phase error: 11.8394917752
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7650625652 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44871265165→41.013 Å
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Refine LS restraints |
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LS refinement shell |
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