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- PDB-8cmp: DNA-binding bacterial histone protein HBB from Bdellovibrio bacte... -

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Basic information

Entry
Database: PDB / ID: 8cmp
TitleDNA-binding bacterial histone protein HBB from Bdellovibrio bacteriovorus
ComponentsCBFD_NFYB_HMF domain-containing protein
KeywordsDNA BINDING PROTEIN / Bacterial Histone
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsHu, Y. / Joiner, J.D. / Albrecht, R. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: 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
DepositionFeb 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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)7,1901
Polymers7,1901
Non-polymers00
Water52229
1
A: CBFD_NFYB_HMF domain-containing protein

A: CBFD_NFYB_HMF domain-containing protein


Theoretical massNumber of molelcules
Total (without water)14,3792
Polymers14,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3000 Å2
ΔGint-34 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.474, 56.345, 26.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CBFD_NFYB_HMF domain-containing protein


Mass: 7189.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Gene: AZI86_06880 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A150WQJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.8 Å3/Da / Density % sol: 31.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate, pH 4.5 and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.06→28.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.778 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16918 1161 5 %RANDOM
Rwork0.14242 ---
obs0.14374 22065 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å20 Å2
2--0.73 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.06→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms436 0 0 29 465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.013445
X-RAY DIFFRACTIONr_bond_other_d0.0020.017492
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.632596
X-RAY DIFFRACTIONr_angle_other_deg1.5771.5971141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.768561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27424.28614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96315105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.165152
X-RAY DIFFRACTIONr_chiral_restr0.1090.266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0275
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1251.41235
X-RAY DIFFRACTIONr_mcbond_other1.6471.402234
X-RAY DIFFRACTIONr_mcangle_it2.1782.119293
X-RAY DIFFRACTIONr_mcangle_other2.262.128294
X-RAY DIFFRACTIONr_scbond_it3.5921.95210
X-RAY DIFFRACTIONr_scbond_other3.5831.961211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4512.689302
X-RAY DIFFRACTIONr_long_range_B_refined3.88517.766476
X-RAY DIFFRACTIONr_long_range_B_other3.89817.647475
X-RAY DIFFRACTIONr_rigid_bond_restr4.0743936
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.063→1.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 59 -
Rwork0.363 1110 -
obs--67.22 %

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