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- PDB-9ezz: Bacterial histone protein HBb from Bdellovibrio bacteriovorus bou... -

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Basic information

Entry
Database: PDB / ID: 9ezz
TitleBacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA
Components
  • DNA (5'-D(P*AP*GP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*CP*T)-3')
  • Transcription factor CBF/NF-Y/archaeal histone domain-containing protein
KeywordsDNA BINDING PROTEIN / Bacterial histone / protein-DNA complex
Function / homologyTranscription 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 speciesBdellovibrio bacteriovorus HD100 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHu, Y. / 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
DepositionApr 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 9, 2024Group: Database references / Structure summary / Category: citation_author / pdbx_entry_details
Item: _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor CBF/NF-Y/archaeal histone domain-containing protein
B: Transcription factor CBF/NF-Y/archaeal histone domain-containing protein
C: DNA (5'-D(P*GP*GP*GP*CP*T)-3')
D: DNA (5'-D(P*AP*GP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1666
Polymers26,9764
Non-polymers1902
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-54 kcal/mol
Surface area8580 Å2
Unit cell
Length a, b, c (Å)32.316, 34.223, 151.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription factor CBF/NF-Y/archaeal histone domain-containing 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 DNA (5'-D(P*GP*GP*GP*CP*T)-3')


Mass: 6494.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*GP*CP*CP*C)-3')


Mass: 6102.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.95→31.63 Å / Num. obs: 12919 / % possible obs: 99.9 % / Redundancy: 7.89 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.104 / Net I/σ(I): 11.3
Reflection shellResolution: 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 / Rrim(I) all: 2.16 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.26805 645 5 %RANDOM
Rwork0.22075 ---
obs0.22295 12274 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.239 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0 Å20 Å2
2--0.95 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.95→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 205 10 40 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131152
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181053
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.5261594
X-RAY DIFFRACTIONr_angle_other_deg1.3271.7372429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0835129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44624.51631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18215187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.662154
X-RAY DIFFRACTIONr_chiral_restr0.0580.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
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_it1.0072.507501
X-RAY DIFFRACTIONr_mcbond_other1.0032.502500
X-RAY DIFFRACTIONr_mcangle_it1.713.736626
X-RAY DIFFRACTIONr_mcangle_other1.7093.742627
X-RAY DIFFRACTIONr_scbond_it1.1433.004649
X-RAY DIFFRACTIONr_scbond_other1.0962.915640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7874.349953
X-RAY DIFFRACTIONr_long_range_B_refined6.651311288
X-RAY DIFFRACTIONr_long_range_B_other6.61830.7621283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1647 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.953→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 47 -
Rwork0.403 888 -
obs--99.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.35360.9387-5.77612.0661-2.429212.2973-0.05350.4564-0.02450.12650.05790.0395-0.19860.145-0.00440.2838-0.052-0.010.1217-0.01060.0322-10.8087-5.060724.9096
210.98191.3197-5.45541.5927-0.74864.9708-0.06850.23610.012-0.01470.04520.0872-0.19170.0690.02330.3636-0.044-0.03050.12-0.01150.0109-9.7921-3.508923.3433
37.29083.6612.76122.13890.58183.4259-0.3176-0.0820.1774-0.1344-0.0281-0.0362-0.455-0.03040.34560.37970.01560.00980.3535-0.05840.3163-0.9567-5.9953-3.3209
412.7007-11.1452-9.347612.07255.023811.6468-1.0592-0.0539-0.94151.1063-0.00590.39920.73640.38151.06510.36320.0026-0.0590.5968-0.09090.31220.5238-10.74652.509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 63
2X-RAY DIFFRACTION2B1 - 62
3X-RAY DIFFRACTION3C2 - 6
4X-RAY DIFFRACTION4D5 - 9

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