+Open data
-Basic information
Entry | Database: PDB / ID: 5g1o | |||||||||
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Title | Aspartate transcarbamoylase domain of human CAD in apo form | |||||||||
Components | CAD protein | |||||||||
Keywords | TRANSFERASE / DE NOVO PYRIMIDINE SYNTHESIS / TRANSCARBAMOYLASE / TRANSCARBAMYLASE / CAD / CARBAMOYL PHOSPHATE SYNTHETASE / DIHYDROOROTASE / COOPERATIVITY | |||||||||
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: 2.1 Å | |||||||||
Authors | Ruiz-Ramos, A. / Grande-Garcia, A. / Moreno-Morcillo, M.D. / Ramon-Maiques, S. | |||||||||
Citation | Journal: Structure / Year: 2016 Title: Structure and Functional Characterization of Human Aspartate Transcarbamoylase, the Target of the Anti-Tumoral Drug Pala. Authors: Ruiz-Ramos, A. / Velazquez-Campoy, A. / Grande-Garcia, A. / Moreno-Morcillo, M. / Ramon-Maiques, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Expression, Purification, Crystallization and Preliminary X- Ray Diffraction Analysis of the Aspartate Transcarbamoylase Domain of Human Cad. Authors: Ruiz-Ramos, A. / Lallous, N. / Grande-Garcia, A. / 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 | 5g1o.cif.gz | 346.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g1o.ent.gz | 282.7 KB | Display | PDB format |
PDBx/mmJSON format | 5g1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g1o_validation.pdf.gz | 488.4 KB | Display | wwPDB validaton report |
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Full document | 5g1o_full_validation.pdf.gz | 513.3 KB | Display | |
Data in XML | 5g1o_validation.xml.gz | 65 KB | Display | |
Data in CIF | 5g1o_validation.cif.gz | 91.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/5g1o ftp://data.pdbj.org/pub/pdb/validation_reports/g1/5g1o | HTTPS FTP |
-Related structure data
Related structure data | 5g1nC 5g1pC 3csuS 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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Unit cell |
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-Components
#1: Protein | Mass: 34911.422 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: HUMAN CDNA PURCHASED FROM OPENBIOSYSTEMS (CLONE ID 5551082) Gene: CAD / Plasmid: POPIN-M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), aspartate carbamoyltransferase, dihydroorotase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | Details: 0.1 M TRIS PH 8.5, 6% PEG 8000, 11% ETHYLENE GLYCOL |
-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 2, 2012 | |||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→42.4 Å / Num. obs: 95831 / % possible obs: 94.3 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9 | |||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.4 / % possible all: 63.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CSU Resolution: 2.1→42.43 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.575 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.018 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42.43 Å
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Refine LS restraints |
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