+Open data
-Basic information
Entry | Database: PDB / ID: 5loj | ||||||||||||
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Title | Structure of full length unliganded CodY from Bacillus subtilis | ||||||||||||
Components | GTP-sensing transcriptional pleiotropic repressor CodY | ||||||||||||
Keywords | TRANSCRIPTION / GAF / wHTH / transcriptional regulator / CodY | ||||||||||||
Function / homology | Function and homology information 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 | Bacillus subtilis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 Å | ||||||||||||
Authors | Wilkinson, A.J. / Levdikov, V.M. / Blagova, E.V. | ||||||||||||
Funding support | United Kingdom, United States, 3items
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Citation | 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. #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: Journal: J. Biol. Chem. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5loj.cif.gz | 218 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5loj.ent.gz | 176.1 KB | Display | PDB format |
PDBx/mmJSON format | 5loj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5loj_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 5loj_full_validation.pdf.gz | 497.9 KB | Display | |
Data in XML | 5loj_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 5loj_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5loj ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5loj | HTTPS FTP |
-Related structure data
Related structure data | 5lnhC 5loeC 5looC 2b0lS 2gx5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 2 - 256 / Label seq-ID: 1 - 255
NCS oper:
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-Components
#1: Protein | Mass: 29604.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: codY, BSU16170 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P39779 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.7M Li2SO4, sodium citrate pH 5.6, 3% dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→25 Å / Num. obs: 8235 / % possible obs: 97.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 33.14 |
Reflection shell | Resolution: 3.7→3.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 5.66 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GX5, 2B0L Resolution: 3.71→24.94 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.83 / SU B: 115.534 / SU ML: 0.82 / Cross valid method: THROUGHOUT / ESU R Free: 1.059 / 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: 83.452 Å2
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Refinement step | Cycle: 1 / Resolution: 3.71→24.94 Å
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Refine LS restraints |
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