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- PDB-2hgv: 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: 2hgv | ||||||
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Title | N-terminal GAF domain of transcriptional pleiotropic repressor CodY | ||||||
![]() | GTP-sensing transcriptional pleiotropic repressor codY | ||||||
![]() | DNA BINDING PROTEIN / 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: 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 | ![]() | 80.5 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.4 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b0lC ![]() 2b18SC ![]() 2gx5C 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18831.396 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-VAL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 5000, calcium acetate, valine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2005 |
Radiation | Monochromator: Silicon (1 1 1) channel-cut / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 7646 / Num. obs: 7646 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.361 / Num. unique all: 672 / % possible all: 92.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2B18 Resolution: 2.3→27.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.285 / SU ML: 0.158 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.249 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→27.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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