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Yorodumi- PDB-5duk: N-terminal structure of putative DNA binding transcription factor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5duk | ||||||
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Title | N-terminal structure of putative DNA binding transcription factor from Thermoplasmatales archaeon SCGC AB-539-N05 | ||||||
Components | putative DNA binding proteinDNA-binding protein | ||||||
Keywords | TRANSCRIPTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / putative DNA binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoplasmatales archaeon SCGC AB-539-N05 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.352 Å | ||||||
Authors | Chang, C. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To Be Published Title: N-terminal structure of putative DNA binding transcription factor from Thermoplasmatales archaeon SCGC AB-539-N05 Authors: Chang, C. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5duk.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5duk.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 5duk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/5duk ftp://data.pdbj.org/pub/pdb/validation_reports/du/5duk | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9241.362 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 7-80) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasmatales archaeon SCGC AB-539-N05 (archaea) Gene: MBGDN05_00160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: M7T6A0 #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: 2.56 Å3/Da / Density % sol: 51.94 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M ammonium Sulfate, 0.1M tri-Sodium chitrate, 15% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→50 Å / Num. obs: 8330 / % possible obs: 99 % / Redundancy: 19.8 % / Biso Wilson estimate: 29.89 Å2 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.029 / Rrim(I) all: 0.128 / Χ2: 1.19 / Net I/av σ(I): 25.26 / Net I/σ(I): 9.9 / Num. measured all: 164940 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.352→39.465 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.79 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.31 Å2 / Biso mean: 34.7873 Å2 / Biso min: 13.69 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.352→39.465 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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