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Yorodumi- PDB-2gx5: N-terminal GAF domain of transcriptional pleiotropic repressor CodY -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gx5 | ||||||
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Title | N-terminal GAF domain of transcriptional pleiotropic repressor CodY | ||||||
Components | GTP-sensing transcriptional pleiotropic repressor codY | ||||||
Keywords | TRANSCRIPTION / CodY / DNA-binding / Nucleotide-binding / Repressor / Transcription regulation / GAF domain / Branched chain amino acid binding | ||||||
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: 1.74 Å | ||||||
Authors | Wilkinson, A.J. / Levdikov, V.M. / Blagova, E.V. | ||||||
Citation | 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. #1: 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. #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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gx5.cif.gz | 296.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gx5.ent.gz | 240.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/2gx5 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/2gx5 | HTTPS FTP |
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-Related structure data
Related structure data | 2b0lC 2b18SC 2hgvC 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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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.) Bacillus subtilis (bacteria) / Gene: codY / Plasmid: pET-YSBLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P39779 |
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-Non-polymers , 7 types, 411 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9757 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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