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Yorodumi- PDB-8bps: Aspartate transcarbamoylase mutant (N2045C, R2238C) from Chaetomi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bps | |||||||||
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Title | Aspartate transcarbamoylase mutant (N2045C, R2238C) from Chaetomium thermophilum CAD-like in apo form | |||||||||
Components | Carbamoyl-phosphate synthase (glutamine-hydrolyzing) | |||||||||
Keywords | TRANSFERASE / Nucleotide metabolism / de novo pyrimidine synthesis / CAD / cysteine / disulfide bridge / protein stability / crosslinking / succinate / multienzymatic protein | |||||||||
Function / homology | Function and homology information carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / hydrolase activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermochaetoides thermophila (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||
Authors | del Cano-Ochoa, F. / Ramon-Maiques, S. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Molecules / Year: 2023 Title: A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD. Authors: Del Cano-Ochoa, F. / Rubio-Del-Campo, 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 | 8bps.cif.gz | 247.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bps.ent.gz | 169.9 KB | Display | PDB format |
PDBx/mmJSON format | 8bps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bps_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 8bps_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 8bps_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 8bps_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bps ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bps | HTTPS FTP |
-Related structure data
Related structure data | 8bplC 5nnnS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 35495.035 Da / Num. of mol.: 1 / Mutation: N2045C, R2238C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0032600 / Plasmid: pOPIN-M-ctATC2Cys / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S583 | ||||||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: Bipyramidal-shaped crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M succinic acid pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→49.08 Å / Num. obs: 325801 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 49.11 Å2 / CC1/2: 1 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 30416 / CC1/2: 0.704 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NNN Resolution: 2.03→49.08 Å / SU ML: 0.2563 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.936 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→49.08 Å
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Refine LS restraints |
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LS refinement shell |
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