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- PDB-1o3q: PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o3q | |||||||||
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Title | PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES | |||||||||
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![]() | GENE REGULATION/DNA / PROTEIN-DNA COMPLEX / CAP / CAP-DNA / CATABOLITE GENE ACTIVATOR PROTEIN / CAMP RECEPTOR PROTEIN / CRP / GENE REGULATION-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 | ![]() ![]() | |||||||||
![]() | Chen, S. / Vojtechovsky, J. / Parkinson, G.N. / Ebright, R.H. / Berman, H.M. | |||||||||
![]() | ![]() Title: Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking Authors: Chen, S. / Vojtechovsky, J. / Parkinson, G.N. / Ebright, R.H. / Berman, H.M. #1: ![]() Title: Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: Alteration of DNA Binding Specificity Through Alteration of DNA Kinking Authors: Chen, S. / Gunasekera, A. / Zhang, X. / Kunkel, T.A. / Ebright, R.H. / Berman, H.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.8 KB | Display | ![]() |
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PDB format | ![]() | 48.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 16.9 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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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3405.273 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 4533.970 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 22558.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.23 Details: PEG 8000, 1,4-DIOXANE, MES, NACL, MGCL2, CAMP, pH 6.23, VAPOR DIFFUSION, HANGING DROP at 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.2 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 9976 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 39.99 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.422 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. obs: 10299 / Num. measured all: 108474 |
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Processing
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Refinement | Resolution: 3→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2648334.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.42 Å2 / ksol: 0.419 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.247 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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