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Yorodumi- PDB-1kaf: DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kaf | ||||||
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Title | DNA Binding Domain Of The Phage T4 Transcription Factor MotA (AA105-211) | ||||||
Components | Transcription regulatory protein MOTA | ||||||
Keywords | TRANSCRIPTION / Escherichia coli / X-ray crystallography / protein-DNA interactions / structural genomics / eubacterial promoters. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Li, N. / Sickmier, E.A. / Zhang, R. / Joachimiak, A. / White, S.W. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2002 Title: The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: the 'double wing' motif. Authors: Li, N. / Sickmier, E.A. / Zhang, R. / Joachimiak, A. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kaf.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kaf.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 1kaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/1kaf ftp://data.pdbj.org/pub/pdb/validation_reports/ka/1kaf | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12538.558 Da / Num. of mol.: 6 / Fragment: DNA binding domain residues 105-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: MotA / Plasmid: pet13a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P22915 #2: 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: 2.06 Å3/Da / Density % sol: 40.39 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: from 19% PEG 8000, 35 mM potassium phosphate pH 5.0, 3% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9789, 0.9636 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 1999 | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→30 Å / Num. obs: 60440 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % | ||||||||||||
Reflection shell | Resolution: 1.6→1.63 Å / % possible all: 92 | ||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 87713 / % possible obs: 92 % / Num. measured all: 638591 / Rmerge(I) obs: 0.1 | ||||||||||||
Reflection shell | *PLUS % possible obs: 83 % / Mean I/σ(I) obs: 6.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 11.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.226 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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