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Yorodumi- PDB-8pbp: Mutant R1785C of the dihydroorotase domain of human CAD protein b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pbp | ||||||||||||
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Title | Mutant R1785C of the dihydroorotase domain of human CAD protein bound to the substrate carbamoyl aspartate | ||||||||||||
Components | CAD protein | ||||||||||||
Keywords | HYDROLASE / Nucleotide metabolism / de novo pyrimidine synthesis / CAD disease / multienzymatic protein / zinc / carboxylated lysine / BIOSYNTHETIC PROTEIN | ||||||||||||
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: 1.54 Å | ||||||||||||
Authors | del Cano-Ochoa, F. / Ramon-Maiques, S. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: J Inherit Metab Dis / Year: 2023 Title: Beyond genetics: Deciphering the impact of missense variants in CAD deficiency. Authors: Del Cano-Ochoa, F. / Ng, B.G. / Rubio-Del-Campo, A. / Mahajan, S. / Wilson, M.P. / Vilar, M. / Rymen, D. / Sanchez-Pintos, P. / Kenny, J. / Ley Martos, M. / Campos, T. / Wortmann, S.B. / ...Authors: Del Cano-Ochoa, F. / Ng, B.G. / Rubio-Del-Campo, A. / Mahajan, S. / Wilson, M.P. / Vilar, M. / Rymen, D. / Sanchez-Pintos, P. / Kenny, J. / Ley Martos, M. / Campos, T. / Wortmann, S.B. / Freeze, H.H. / 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 | 8pbp.cif.gz | 251.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pbp.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 8pbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/8pbp ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pbp | HTTPS FTP |
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-Related structure data
Related structure data | 8pbeC 8pbgC 8pbhC 8pbiC 8pbjC 8pbkC 8pbmC 8pbnC 8pbqC 8pbrC 8pbsC 8pbtC 8pbuC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39640.375 Da / Num. of mol.: 1 / Mutation: R1785C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Plasmid: pOPIN-M-huDHO-R1785C / Cell (production host): epithelial-like / Cell line (production host): HEK293 GnTI / Organ (production host): Embryo / Production host: Homo sapiens (human) / Tissue (production host): Kidney References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), aspartate carbamoyltransferase, dihydroorotase |
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-Non-polymers , 5 types, 252 molecules
#2: Chemical | ChemComp-NCD / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-DOR / ( | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES pH 7, 2.8 M sodium formate, 2 mM carbamoyl aspartate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→48.72 Å / Num. obs: 59225 / % possible obs: 98.74 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.19 |
Reflection shell | Resolution: 1.54→1.595 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 5377 / CC1/2: 0.568 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→48.72 Å / SU ML: 0.2197 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8913 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→48.72 Å
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Refine LS restraints |
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LS refinement shell |
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