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Yorodumi- PDB-5nnl: Inactive dihydroorotase-like domain of Chaetomium thermophilum CA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nnl | |||||||||
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Title | Inactive dihydroorotase-like domain of Chaetomium thermophilum CAD-like multifunctional protein | |||||||||
Components | Inactive dihydroorotase-like domain | |||||||||
Keywords | OXIDOREDUCTASE / TIM-barrel / de novo pyrimidine biosynthesis / 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: 2.13 Å | |||||||||
Authors | Ramon-Maiques, S. / Moreno-Morcillo, M. / Grande-Garcia, A. | |||||||||
Funding support | Spain, 2items
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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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nnl.cif.gz | 258.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nnl.ent.gz | 211 KB | Display | PDB format |
PDBx/mmJSON format | 5nnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nnl_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 5nnl_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 5nnl_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 5nnl_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/5nnl ftp://data.pdbj.org/pub/pdb/validation_reports/nn/5nnl | HTTPS FTP |
-Related structure data
Related structure data | 5nnnC 5nnqC 4c6mS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37377.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0032600 / Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G0S583 #2: 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: 2.18 Å3/Da / Density meas: 2.18 Mg/m3 / Density % sol: 44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: A construct spanning the DHO-like and ATC domains of C. thermophilum CAD-like protein was used for crystallization at 5 mg/ml. Crystals appear after 2-3 weeks in conditions with 20% PEG ...Details: A construct spanning the DHO-like and ATC domains of C. thermophilum CAD-like protein was used for crystallization at 5 mg/ml. Crystals appear after 2-3 weeks in conditions with 20% PEG 20,000 and 0.1 M citric acid pH 4.5. The crystals only contained the DHO-like domain of the construct that was cleaved off during crystallization. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.93927 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93927 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→48 Å / Num. obs: 36234 / % possible obs: 98.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.13→2.25 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2 / Num. unique obs: 5197 / CC1/2: 0.702 / Rpim(I) all: 0.411 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C6M Resolution: 2.13→45.814 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→45.814 Å
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Refine LS restraints |
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LS refinement shell |
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