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Yorodumi- PDB-3w6v: Crystal structure of the DNA-binding domain of AdpA, the global t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w6v | ||||||
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Title | Crystal structure of the DNA-binding domain of AdpA, the global transcriptional factor, in complex with a target DNA | ||||||
Components |
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Keywords | TRANSCRIPTION ACTIVATOR/DNA / H-T-H motif / sequence-specific DNA binding transcription factor activity / DNA-binding / intracellular / TRANSCRIPTION ACTIVATOR-DNA complex | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Yao, M.D. / Ohtsuka, J. / Nagata, K. / Miyazono, K. / Ohnishi, Y. / Tanokura, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity Authors: Yao, M.D. / Ohtsuka, J. / Nagata, K. / Miyazono, K. / Zhi, Y. / Ohnishi, Y. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w6v.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w6v.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 3w6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/3w6v ftp://data.pdbj.org/pub/pdb/validation_reports/w6/3w6v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16743.789 Da / Num. of mol.: 1 / Fragment: DNA-binding domain, residues 215-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: adpA / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9S166 |
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#2: DNA chain | Mass: 4828.146 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 4970.213 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.1M sodium HEPES, 10%(v/v) 2-propanol, 16%(w/v) PEG4000, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 7, 2010 / Details: diffraction |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 10045 / Num. obs: 9885 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.93 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 11.93 / Num. unique all: 10045 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D5Y, 1BL0 Resolution: 2.95→19.5 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / SU B: 15.543 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.655 / ESU R Free: 0.367 / 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: 66.487 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→19.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.025 Å / Total num. of bins used: 20
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