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- PDB-1run: CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1run | ||||||
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Title | CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE | ||||||
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![]() | TRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / 3D-STRUCTURE / DNA-BINDING / CAMP-BINDING / ACTIVATOR / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription ...carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Parkinson, G.N. / Gunasekera, A. / Vojtechovsky, J. / Zhang, X. / Kunkel, T.A. / Berman, H.M. / Ebright, R.H. | ||||||
![]() | ![]() Title: Aromatic hydrogen bond in sequence-specific protein DNA recognition. Authors: Parkinson, G. / Gunasekera, A. / Vojtechovsky, J. / Zhang, X. / Kunkel, T.A. / Berman, H. / Ebright, R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.8 KB | Display | ![]() |
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PDB format | ![]() | 99.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1018.6 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 4352.867 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 5152.358 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 23541.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 58.68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 258 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Sep 1, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 17777 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.116 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 40 Å / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Num. measured all: 48657 |
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Processing
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Refinement | Resolution: 2.7→10 Å / σ(F): 4
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Software | *PLUS Name: ![]() | ||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(F): 4 / Rfactor obs: 0.207 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS Biso mean: 26.7 Å2 | ||||||||||||
Refine LS restraints | *PLUS
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