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Yorodumi- PDB-9ezz: Bacterial histone protein HBb from Bdellovibrio bacteriovorus bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ezz | ||||||
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Title | Bacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA | ||||||
Components |
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Keywords | 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 Function and homology information | ||||||
Biological species | Bdellovibrio bacteriovorus HD100 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hu, Y. / Albrecht, R. / Hartmann, M.D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ezz.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ezz.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 9ezz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ezz_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 9ezz_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 9ezz_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 9ezz_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/9ezz ftp://data.pdbj.org/pub/pdb/validation_reports/ez/9ezz | HTTPS FTP |
-Related structure data
Related structure data | 9f0eC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Bdellovibrio bacteriovorus HD100 (bacteria) Gene: Bd0055 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MRM1 #2: DNA chain | | Mass: 6494.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 6102.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.0, 0.2 M LiCl and 20% PEG 6k |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 20, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→31.63 Å / Num. obs: 12919 / % possible obs: 99.9 % / Redundancy: 7.89 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 8.33 % / Rmerge(I) obs: 2.02 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 2021 / CC1/2: 0.482 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→31.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.273 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 48.239 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→31.63 Å
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