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- PDB-9f0e: Bacterial histone protein HBb from Bdellovibrio bacteriovorus bou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9f0e | ||||||
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Title | Bacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA | ||||||
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![]() | DNA BINDING PROTEIN / Bacterial histone / 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 / PHOSPHATE ION / DNA / DNA (> 10) / Transcription factor CBF/NF-Y/archaeal histone domain-containing protein![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hu, Y. / Albrecht, R. / Hartmann, M.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Authors: Hu, Y. / Schwab, S. / Deiss, S. / Escudeiro, P. / van Heesch, T. / Joiner, J.D. / Vreede, J. / Hartmann, M.D. / Lupas, A.N. / Alvarez, B.H. / Alva, V. / Dame, R.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 | ![]() | 71.4 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.3 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 | ![]() 9ezzC 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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Unit cell |
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Components
#1: Protein | Mass: 7189.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Bd0055 / Production host: ![]() ![]() #2: DNA chain | | Mass: 6102.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate and 22% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→42.49 Å / Num. obs: 16780 / % possible obs: 93 % / Redundancy: 4.68 % / CC1/2: 0.996 / Rrim(I) all: 0.11 / Net I/σ(I): 9.59 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.18 / Num. unique obs: 2747 / CC1/2: 0.914 / Rrim(I) all: 0.637 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.284 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→42.49 Å
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Refine LS restraints |
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