[English] 日本語
Yorodumi- PDB-8gw0: Crystal structure of the human dihydroorotase domain in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gw0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human dihydroorotase domain in complex with malic acid | ||||||
Components | CAD protein | ||||||
Keywords | HYDROLASE / dihydroorotase / Human CAD / ZN | ||||||
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: 1.64 Å | ||||||
Authors | Yang, P.C. / Liu, H.W. / Huang, H.Y. / Huang, C.Y. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Biomolecules / Year: 2023 Title: Complexed Crystal Structure of the Dihydroorotase Domain of Human CAD Protein with the Anticancer Drug 5-Fluorouracil. Authors: Lin, E.S. / Huang, Y.H. / Yang, P.C. / Peng, W.F. / Huang, C.Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gw0.cif.gz | 93 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gw0.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 8gw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/8gw0 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/8gw0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8gvzC 5ynzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42761.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P27708, dihydroorotase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-LMR / ( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.84 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M DL-Malic acid, pH 6.0, 1.6M potassium sodium tartrate tetrahydrate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→30 Å / Num. obs: 48819 / % possible obs: 98.8 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 11.51 |
Reflection shell | Resolution: 1.64→1.74 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.12 / Num. unique obs: 51300 / CC1/2: 0.807 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YNZ Resolution: 1.64→28.53 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.86 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.67 Å2 / Biso mean: 28.769 Å2 / Biso min: 16.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.64→28.53 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|