+Open data
-Basic information
Entry | Database: PDB / ID: 8fvx | ||||||
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Title | Histone from Bdellovibrio bacteriovorus | ||||||
Components | CBFD_NFYB_HMF domain-containing protein | ||||||
Keywords | DNA BINDING PROTEIN / Histone / NAP | ||||||
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 Function and homology information | ||||||
Biological species | Bdellovibrio bacteriovorus HD100 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Laursen, S.P. / Luger, K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Microbiol / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fvx.cif.gz | 28.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fvx.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 8fvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fvx_validation.pdf.gz | 410 KB | Display | wwPDB validaton report |
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Full document | 8fvx_full_validation.pdf.gz | 410 KB | Display | |
Data in XML | 8fvx_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 8fvx_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/8fvx ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fvx | HTTPS FTP |
-Related structure data
Related structure data | 8fw7C 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: 6994.307 Da / Num. of mol.: 1 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 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.11 % / Description: Flat rhomboid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 3.2 M (NH4)2SO4, 100 mM BICINE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→29.39 Å / Num. obs: 5959 / % possible obs: 86.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 9.63 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05163 / Rpim(I) all: 0.01851 / Rrim(I) all: 0.05496 / Net I/av σ(I): 26.79 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.8→1.865 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.1029 / Mean I/σ(I) obs: 10.42 / Num. unique obs: 2407 / CC1/2: 0.991 / CC star: 0.998 / Rpim(I) all: 0.04756 / Rrim(I) all: 0.114 / % possible all: 95.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.39 Å / SU ML: 0.1447 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.5642 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.61 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.39 Å
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Refine LS restraints |
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LS refinement shell |
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