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Yorodumi- PDB-1o3s: PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o3s | |||||||||
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Title | PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES | |||||||||
Components |
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Keywords | GENE REGULATION/DNA / PROTEIN-DNA COMPLEX / CAP / CAP-DNA / CATABOLITE GENE ACTIVATOR PROTEIN / CAMP RECEPTOR PROTEIN / CRP / GENE REGULATION-DNA COMPLEX | |||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | |||||||||
Authors | Chen, S. / Ebright, R.H. / Berman, H.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 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. #1: Journal: J.Mol.Biol. / Year: 2001 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o3s.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o3s.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 1o3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/1o3s ftp://data.pdbj.org/pub/pdb/validation_reports/o3/1o3s | 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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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3390.262 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 4549.969 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 22544.047 Da / Num. of mol.: 1 / Mutation: GLU181ASP Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACJ8 | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 / Details: Chen, S., (2001) J.Mol.Biol., 314, 63. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
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: 10382 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 48.23 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.41 / % possible all: 94.3 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. all: 10511 / Num. obs: 10352 / Num. measured all: 108811 |
-Processing
Software |
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Refinement | Resolution: 3→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2545210.69 / 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: 34.27 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.4 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: 0.031 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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