[English] 日本語
Yorodumi- PDB-5hs7: Reduced form of the transcriptional regulator YodB from B. subtilis -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hs7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Reduced form of the transcriptional regulator YodB from B. subtilis | ||||||||||||
Components | HTH-type transcriptional regulator YodB | ||||||||||||
Keywords | DNA BINDING PROTEIN / HTH-type transcriptional regulator / reduced form | ||||||||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription Similarity search - Function | ||||||||||||
Biological species | Bacillus subtilis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Lee, S.J. / Lee, I.G. / Lee, B.J. | ||||||||||||
Funding support | Korea, Republic Of, 3items
| ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Two distinct mechanisms of transcriptional regulation by the redox sensor YodB Authors: Lee, S.J. / Lee, I.G. / Lee, K.Y. / Kim, D.G. / Eun, H.J. / Yoon, H.J. / Chae, S. / Song, S.H. / Kang, S.O. / Seo, M.D. / Kim, H.S. / Park, S.J. / Lee, B.J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hs7.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hs7.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/5hs7 ftp://data.pdbj.org/pub/pdb/validation_reports/hs/5hs7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5hs8C 5hs9C 4hqmS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12725.838 Da / Num. of mol.: 2 / Fragment: UNP residues 5-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yodB, BSU19540 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O34844 #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M sodium bromide and 20%(w/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50.12 Å / Num. obs: 22351 / % possible obs: 99 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 44.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.451 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HQM Resolution: 1.7→50.12 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.391 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.782 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|