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- PDB-8cmp: DNA-binding bacterial histone protein HBB from Bdellovibrio bacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cmp | ||||||
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Title | DNA-binding bacterial histone protein HBB from Bdellovibrio bacteriovorus | ||||||
![]() | CBFD_NFYB_HMF domain-containing protein | ||||||
![]() | DNA BINDING PROTEIN / Bacterial Histone | ||||||
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 / Transcription factor CBF/NF-Y/archaeal histone domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hu, Y. / Joiner, J.D. / Albrecht, R. / Hartmann, M.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic resolution structure of a DNA-binding bacterial histone from Bdellovibrio bacteriovorus Authors: Hu, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.3 KB | Display | ![]() |
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PDB format | ![]() | 23.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.4 KB | Display | ![]() |
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Full document | ![]() | 408.3 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate, pH 4.5 and 25% PEG3350 |
-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: Sep 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→28.2 Å / Num. obs: 23226 / % possible obs: 96.3 % / Redundancy: 10.8 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.06→1.13 Å / Redundancy: 3.88 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 3028 / CC1/2: 0.688 / Rrim(I) all: 0.921 / % possible all: 79.4 |
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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: 17.722 Å2
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Refinement step | Cycle: 1 / Resolution: 1.06→28.19 Å
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Refine LS restraints |
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