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- PDB-8fvx: Histone from Bdellovibrio bacteriovorus -

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Basic information

Entry
Database: PDB / ID: 8fvx
TitleHistone from Bdellovibrio bacteriovorus
ComponentsCBFD_NFYB_HMF domain-containing protein
KeywordsDNA BINDING PROTEIN / Histone / NAP
Function / homologyTranscription 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 speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLaursen, S.P. / Luger, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionJan 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBFD_NFYB_HMF domain-containing protein


Theoretical massNumber of molelcules
Total (without water)6,9941
Polymers6,9941
Non-polymers00
Water77543
1
A: CBFD_NFYB_HMF domain-containing protein

A: CBFD_NFYB_HMF domain-containing protein


Theoretical massNumber of molelcules
Total (without water)13,9892
Polymers13,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_566x,-y+1,-z+11
Buried area3660 Å2
ΔGint-36 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.772, 34.412, 56.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein CBFD_NFYB_HMF domain-containing 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.11 % / Description: Flat rhomboid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 3.2 M (NH4)2SO4, 100 mM BICINE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data collection
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building
Cootmodel building
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2331 461 -
Rwork0.1889 4640 -
obs-5156 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms476 0 0 43 519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069476
X-RAY DIFFRACTIONf_angle_d0.8158636
X-RAY DIFFRACTIONf_chiral_restr0.053483
X-RAY DIFFRACTIONf_plane_restr0.004877
X-RAY DIFFRACTIONf_dihedral_angle_d4.939564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.980.24281230.19521107X-RAY DIFFRACTION98.16
1.98-2.270.2361270.17521140X-RAY DIFFRACTION100
2.27-2.860.26731290.20161160X-RAY DIFFRACTION99.77
2.86-29.390.21061370.18321233X-RAY DIFFRACTION99.71

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