[English] 日本語
Yorodumi- PDB-5n0l: The structure of the cofactor binding GAF domain of the nutrient ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n0l | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile | |||||||||
Components | GTP-sensing transcriptional pleiotropic repressor CodY | |||||||||
Keywords | TRANSCRIPTION / Nutrient sensor / transcription regulation / GAF domain / clostridium | |||||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / GTP binding / DNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Clostridioides difficile (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Levdikov, V.M. / Blagova, E.V. / Wilkinson, A.J. / Sonenshein, A.L. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: Plos One / Year: 2019 Title: Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027. Authors: Daou, N. / Wang, Y. / Levdikov, V.M. / Nandakumar, M. / Livny, J. / Bouillaut, L. / Blagova, E. / Zhang, K. / Belitsky, B.R. / Rhee, K. / Wilkinson, A.J. / Sun, X. / Sonenshein, A.L. #1: Journal: J. Biol. Chem. / Year: 2017 Title: Structure of the Branched-chain Amino Acid and GTP-sensing Global Regulator, CodY, from Bacillus subtilis. Authors: Levdikov, V.M. / Blagova, E. / Young, V.L. / Belitsky, B.R. / Lebedev, A. / Sonenshein, A.L. / Wilkinson, A.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5n0l.cif.gz | 413.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5n0l.ent.gz | 340.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/5n0l ftp://data.pdbj.org/pub/pdb/validation_reports/n0/5n0l | HTTPS FTP |
---|
-Related structure data
Related structure data | 2b18S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17355.488 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: codY, BN1095_790003, BN1096_560190, BN1097_540194 / Plasmid: pET-YSBLIC-3C / Details (production host): encodes cleavage his tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A031WD25, UniProt: Q18BE1*PLUS #2: Chemical | ChemComp-ILE / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.84 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% polyethylene glycol 3350, 0.2 M sodium formate, 0.1 M Bis-tris-propane, pH 6.5 and protein solutions containing 10 mM isoleucine. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→56.19 Å / Num. obs: 115569 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.68→1.72 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.81 / Num. unique obs: 8396 / CC1/2: 0.515 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B18 Resolution: 1.68→56.19 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.491 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.644 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.68→56.19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|