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Yorodumi- PDB-5loe: Structure of full length Cody from Bacillus subtilis in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5loe | ||||||||||||
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Title | Structure of full length Cody from Bacillus subtilis in complex with Ile | ||||||||||||
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 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 | 5loe.cif.gz | 424.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5loe.ent.gz | 355.5 KB | Display | PDB format |
PDBx/mmJSON format | 5loe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5loe ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5loe | HTTPS FTP |
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-Related structure data
Related structure data | 5lnhC 5lojC 5looC 2b0lS 2b18S 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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2 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 29301.377 Da / Num. of mol.: 4 / Mutation: L3S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: codY, BSU16170 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P39779 #2: Chemical | ChemComp-ILE / #3: Water | ChemComp-HOH / | |
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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: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG5000, 0.1M HEPES pH 7.5, 5% tacsimate, 20mM Ile |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 22830 / % possible obs: 92.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 0.96 / % possible all: 47.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B18, 2B0L Resolution: 3→45.45 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 65.422 / SU ML: 0.505 / Cross valid method: THROUGHOUT / ESU R Free: 0.582 / 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: 110.383 Å2
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Refinement step | Cycle: 1 / Resolution: 3→45.45 Å
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Refine LS restraints |
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