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Open data
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Basic information
Entry | Database: PDB / ID: 5loo | ||||||||||||
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Title | Structure of full length unliganded CodY from Bacillus subtilis | ||||||||||||
![]() | GTP-sensing transcriptional pleiotropic repressor CodY | ||||||||||||
![]() | TRANSCRIPTION / GAF / wHTH / transcriptional regulator / CodY | ||||||||||||
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. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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. #1: Journal: J. Mol. Biol. / Year: 2009 Title: Structural rearrangement accompanying ligand binding in the GAF domain of CodY from Bacillus subtilis. Authors: Levdikov, V.M. / Blagova, E. / Colledge, V.L. / Lebedev, A.A. / Williamson, D.C. / Sonenshein, A.L. / Wilkinson, A.J. #2: ![]() 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. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 682.3 KB | Display | ![]() |
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PDB format | ![]() | 567.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 512.4 KB | Display | ![]() |
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Full document | ![]() | 696.9 KB | Display | |
Data in XML | ![]() | 88.1 KB | Display | |
Data in CIF | ![]() | 130.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lnhC ![]() 5loeC ![]() 5lojSC C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 29604.713 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1M sodium citrate pH6.0, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9804 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→20 Å / Num. obs: 29671 / % possible obs: 71.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.77 |
Reflection shell | Resolution: 4.5→4.58 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.01 / % possible all: 71.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LOJ Resolution: 4.5→19.88 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.824 / SU B: 165.968 / SU ML: 2.029 / Cross valid method: THROUGHOUT / ESU R Free: 1.999 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 235.091 Å2
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Refinement step | Cycle: 1 / Resolution: 4.5→19.88 Å
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Refine LS restraints |
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