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Yorodumi- PDB-5nnq: Aspartate transcarbamoylase from Chaetomium thermophilum CAD-like... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nnq | ||||||
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Title | Aspartate transcarbamoylase from Chaetomium thermophilum CAD-like bound to carbamoyl phosphate | ||||||
Components | ctATC | ||||||
Keywords | TRANSFERASE / Carbamoyl phosphate / transcarbamoylase superfamily / CAD / Ura2 | ||||||
Function / homology | Function and homology information carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / citrulline biosynthetic process / aspartate carbamoyltransferase activity / dihydroorotase activity / UTP biosynthetic process / amino acid binding / glutamine metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / ATP binding ...carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / citrulline biosynthetic process / aspartate carbamoyltransferase activity / dihydroorotase activity / UTP biosynthetic process / amino acid binding / glutamine metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Moreno-Morcillo, M. / Grande-Garcia, A. / Ramon-Maiques, S. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Structure / Year: 2017 Title: Structural Insight into the Core of CAD, the Multifunctional Protein Leading De Novo Pyrimidine Biosynthesis. Authors: Moreno-Morcillo, M. / Grande-Garcia, A. / Ruiz-Ramos, A. / Del Cano-Ochoa, F. / Boskovic, J. / Ramon-Maiques, S. #1: Journal: To Be Published Title: Structural insight into the core of CAD, the multifunctional protein leading de novo pyrimidine biosynthesis Authors: Moreno-Morcillo, M. / Grande-Garcia, A. / Ruiz-Ramos, A. / del Cano-Ochoa, F. / Boskovic, J. / 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 | 5nnq.cif.gz | 129.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nnq.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/5nnq ftp://data.pdbj.org/pub/pdb/validation_reports/nn/5nnq | HTTPS FTP |
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-Related structure data
Related structure data | 5nnlC 5nnnC 5g1nS 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: 35560.051 Da / Num. of mol.: 1 / Fragment: UNP Residues 1939-2253 Source method: isolated from a genetically manipulated source Details: Synthetic gene / Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0032600 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G0S583 | ||
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#2: Chemical | #3: 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: 3.27 Å3/Da / Density % sol: 62.42 % / Description: Diamond shape |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.8 M succinic acid pH 7.0 Soaking with carbamoyl phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.91976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91976 Å / Relative weight: 1 |
Reflection | Resolution: 1.797→49.28 Å / Num. obs: 43537 / % possible obs: 99.67 % / Redundancy: 39.1 % / Biso Wilson estimate: 35.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1738 / Rpim(I) all: 0.02807 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.797→1.862 Å / Redundancy: 38.7 % / Rmerge(I) obs: 11.39 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 4235 / CC1/2: 0.209 / Rpim(I) all: 1.829 / % possible all: 96.91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G1N Resolution: 2.26→49.016 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→49.016 Å
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Refine LS restraints |
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LS refinement shell |
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