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Open data
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Basic information
Entry | Database: PDB / ID: 4itq | ||||||
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Title | Crystal structure of hypothetical protein SCO1480 bound to DNA | ||||||
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![]() | GENE REGULATION / STRUCTURAL PROTEIN/DNA / protein-DNA complex / H2TH motif / nucleoid-associated protein / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | ![]() nucleoid / chromosome condensation / ribosome / structural constituent of ribosome / translation / DNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guarne, A. / Nanji, T. / Gloyd, M. / Swiercz, J.P. / Elliot, M.A. | ||||||
![]() | ![]() Title: A novel nucleoid-associated protein specific to the actinobacteria. Authors: Swiercz, J.P. / Nanji, T. / Gloyd, M. / Guarne, A. / Elliot, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.1 KB | Display | ![]() |
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PDB format | ![]() | 25.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.3 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: Protein | Mass: 11717.030 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: protein is MSE-labeled / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 2388.569 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 2468.617 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
Sequence details | THE ORIGINAL SEQUENCE OF THE DNA DUPLEX INCLUDED IN THE CRYSTALLIZATION DROPS IS: 5' ...THE ORIGINAL SEQUENCE OF THE DNA DUPLEX INCLUDED IN THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 19% PEG 3350, 210 mM KSCN, 5% ethylene glycol, 100 mM HEPES pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 5202 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 31.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.37 Å2 / ksol: 0.265 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→29.439 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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