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- PDB-1ca6: INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ca6 | ||||||
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Title | INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA | ||||||
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![]() | STRUCTURAL PROTEIN/DNA / HYPERTHERMOPHILE / CHROMOSOMAL PROTEIN / SSO7D / SAC7D / DNA BINDING / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Su, S. / Gao, Y.-G. / Robinson, H. / Shriver, J.W. / Wang, A.H.-J. | ||||||
![]() | ![]() Title: Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs Authors: Su, S. / Gao, Y.-G. / Robinson, H. / Liaw, Y.C. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.-J. #1: ![]() Title: The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Authors: Robinson, H. / Gao, Y.G. / McCrary, B.S. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H. #2: ![]() Title: The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Authors: Gao, Y.G. / Su, S.Y. / Robinson, H. / Padmanabhan, S. / Lim, L. / McCrary, B.S. / Edmondson, S.P. / Shriver, J.W. / Wang, A.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 | ![]() | 38.3 KB | Display | ![]() |
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PDB format | ![]() | 23.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.1 KB | Display | ![]() |
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Full document | ![]() | 371.6 KB | Display | |
Data in XML | ![]() | 3.2 KB | Display | |
Data in CIF | ![]() | 4.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c8cC ![]() 1ca5C ![]() 1azpS S: Starting model for refinement C: citing same article ( |
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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: 2442.616 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Protein | | Mass: 7626.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 1, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→40 Å / Num. obs: 8013 / % possible obs: 84.4 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.058 |
Reflection | *PLUS Highest resolution: 2.2 Å |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 72.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AZP Resolution: 2.2→8 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 41.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.33 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5.2 % / Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.402 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.353 |