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Yorodumi- PDB-3bwg: The crystal structure of possible transcriptional regulator YydK ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bwg | ||||||
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Title | The crystal structure of possible transcriptional regulator YydK from Bacillus subtilis subsp. subtilis str. 168 | ||||||
Components | Uncharacterized HTH-type transcriptional regulator yydK | ||||||
Keywords | TRANSCRIPTION REGULATOR / APC85486 / YydK / transcriptional regulator / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å | ||||||
Authors | Tan, K. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of possible transcriptional regulator YydK from Bacillus subtilis subsp. subtilis str. 168. Authors: Tan, K. / Zhou, M. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bwg.cif.gz | 148.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bwg.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/3bwg ftp://data.pdbj.org/pub/pdb/validation_reports/bw/3bwg | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27721.912 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Species: Bacillus subtilis / Strain: 168 / Gene: yydK, BSU40130 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q45591 #2: Chemical | ChemComp-EDO / #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: 2.33 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Ammonium acetate, 0.1M Bis-Tris, 17% PEG 10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→43.98 Å / Num. all: 40580 / Num. obs: 40580 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.09→2.18 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.65 / Num. unique all: 1941 / % possible all: 43.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.09→43.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.516 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.246 / ESU R Free: 0.193 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.851 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→43.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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