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- PDB-1c0w: CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRES... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1c0w | ||||||
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Title | CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN | ||||||
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![]() | GENE REGULATION/DNA / TOXIN REPRESSOR-DNA COMPLEX / METAL BINDING SH-LIKE DOMAIN / GENE REGULATION-DNA COMPLEX | ||||||
Function / homology | ![]() transition metal ion binding / SH3 domain binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pohl, E. / Holmes, R.K. / Hol, W.G. | ||||||
![]() | ![]() Title: Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain. Authors: Pohl, E. / Holmes, R.K. / Hol, W.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.7 KB | Display | ![]() |
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PDB format | ![]() | 127 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.8 KB | Display | ![]() |
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Full document | ![]() | 529 KB | Display | |
Data in XML | ![]() | 32.9 KB | Display | |
Data in CIF | ![]() | 44.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dtr S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 6397.159 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6437.183 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 25218.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-CO / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.39 Å3/Da / Density % sol: 77.18 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 3.2 Å |
Reflection | *PLUS % possible obs: 100 % / Num. measured all: 772772 / Rmerge(I) obs: 0.12 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DTR ![]() 1dtr Resolution: 3.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.13 |