+Open data
-Basic information
Entry | Database: PDB / ID: 5g1n | ||||||
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Title | Aspartate transcarbamoylase domain of human CAD bound to PALA | ||||||
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 / 'de novo' UMP biosynthetic process / animal organ regeneration / 'de novo' pyrimidine nucleobase biosynthetic process / 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 / identical protein binding / membrane / nucleus / cytosol / cytoplasm 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 | 5g1n.cif.gz | 361 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g1n.ent.gz | 297.2 KB | Display | PDB format |
PDBx/mmJSON format | 5g1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/5g1n ftp://data.pdbj.org/pub/pdb/validation_reports/g1/5g1n | HTTPS FTP |
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-Related structure data
Related structure data | 5g1oC 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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2 |
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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 5 551082) Plasmid: POPIN-M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: P27708, dihydroorotase, aspartate carbamoyltransferase #2: Chemical | ChemComp-PAL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | Details: 10% ZNCL2, 15% PEG6000, 50 MM SODIUM ACETATE PH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.148 | |||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2013 | |||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.148 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 92437 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9 | |||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CSU Resolution: 2.1→41.58 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.712 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.038 / 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: 36.506 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→41.58 Å
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Refine LS restraints |
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