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- PDB-2gx5: N-terminal GAF domain of transcriptional pleiotropic repressor CodY -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gx5 | ||||||
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Title | N-terminal GAF domain of transcriptional pleiotropic repressor CodY | ||||||
![]() | GTP-sensing transcriptional pleiotropic repressor codY | ||||||
![]() | TRANSCRIPTION / CodY / DNA-binding / Nucleotide-binding / Repressor / Transcription regulation / GAF domain / Branched chain amino acid binding | ||||||
Function / homology | ![]() DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilkinson, A.J. / Levdikov, V.M. / Blagova, E.V. | ||||||
![]() | ![]() Title: The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria. Authors: Levdikov, V.M. / Blagova, E. / Joseph, P. / Sonenshein, A.L. / Wilkinson, A.J. #1: ![]() Title: The Structure of CodY, a GTP- and Isoleucine-responsive Regulator of Stationary Phase and Virulence in Gram-positive Bacteria Authors: Levdikov, V.M. / Blagova, E. / Joseph, P. / Sonenshein, A.L. / Wilkinson, A.J. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization of the GTP-dependent transcriptional regulator CodY from Bacillus subtilis Authors: Blagova, E.V. / Levdikov, V.M. / Tachikawa, K. / Sonenshein, A.L. / Wilkinson, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 296.3 KB | Display | ![]() |
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PDB format | ![]() | 240.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1020.9 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.2 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b0lC ![]() 2b18SC ![]() 2hgvC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 19296.902 Da / Num. of mol.: 4 / Fragment: N-terminal domain, residues 1-159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 411 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PCG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PCG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-P6G / | #7: Chemical | ChemComp-PCG / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium sulphate, sodium citrate, PEG 400, 20mM cGMP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2005 |
Radiation | Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9757 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. all: 85808 / Num. obs: 85808 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.11 |
Reflection shell | Resolution: 1.74→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.67 / Num. unique all: 8202 / % possible all: 95.2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2B18 Resolution: 1.74→31.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.518 / SU ML: 0.067 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.161 / ESU R Free: 0.106 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→31.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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