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Open data
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Basic information
Entry | Database: PDB / ID: 8fw7 | ||||||
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Title | Histone from Bdellovibrio bacteriovorus bound to dsDNA | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Histone / nucleosome / scaffold / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone-fold / protein heterodimerization activity / DNA / Transcription factor CBF/NF-Y/archaeal histone domain-containing protein![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Laursen, S.P. / Luger, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus. Authors: Hocher, A. / Laursen, S.P. / Radford, P. / Tyson, J. / Lambert, C. / Stevens, K.M. / Montoya, A. / Shliaha, P.V. / Picardeau, M. / Sockett, R.E. / Luger, K. / Warnecke, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.7 KB | Display | ![]() |
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PDB format | ![]() | 27.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.6 KB | Display | ![]() |
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Full document | ![]() | 442.7 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fvxC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: DNA chain | Mass: 861.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
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#2: Protein | Mass: 6994.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Bd0055 / Production host: ![]() ![]() #3: DNA chain | | Mass: 572.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | Sequence details | The authors state that the complex was crystallized with 35 bp of dsDNA ...The authors state that the complex was crystallized with 35 bp of dsDNA (TCTTGCACTA | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.66 % / Description: Cubic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% PEG 550 MME, 50 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2022 |
Radiation | Monochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.79 Å / Num. obs: 13147 / % possible obs: 98.37 % / Redundancy: 7.1 % / Biso Wilson estimate: 35.83 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06045 / Rpim(I) all: 0.0249 / Rrim(I) all: 0.06554 / Net I/σ(I): 16.49 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.5857 / Mean I/σ(I) obs: 3.86 / Num. unique obs: 1302 / CC1/2: 0.908 / CC star: 0.976 / Rpim(I) all: 0.2299 / Rrim(I) all: 0.6299 / % possible all: 97.89 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→27.79 Å
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Refine LS restraints |
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LS refinement shell |
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