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- PDB-9f0e: Bacterial histone protein HBb from Bdellovibrio bacteriovorus bou... -

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Basic information

Entry
Database: PDB / ID: 9f0e
TitleBacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA
Components
  • DNA (5'-D(P*CP*GP*TP*TP*AP*AP*AP*GP*C)-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: 1.85 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 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
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*CP*GP*TP*TP*AP*AP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7676
Polymers20,4823
Non-polymers2853
Water1,18966
1
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*CP*GP*TP*TP*AP*AP*AP*GP*C)-3')
hetero molecules

C: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)26,8707
Polymers26,5854
Non-polymers2853
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)108.697, 34.755, 56.433
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number5
Space group name H-MC121

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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*CP*GP*TP*TP*AP*AP*AP*GP*C)-3')


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


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate and 22% PEG 4000

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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: Oct 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.85→42.49 Å / Num. obs: 16780 / % possible obs: 93 % / Redundancy: 4.68 % / CC1/2: 0.996 / Rrim(I) all: 0.11 / Net I/σ(I): 9.59
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.18 / Num. unique obs: 2747 / CC1/2: 0.914 / Rrim(I) all: 0.637 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.49 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.348 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26744 843 5 %RANDOM
Rwork0.24868 ---
obs0.24959 15932 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.284 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å20.27 Å2
2---2.31 Å20 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.85→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 170 15 66 1113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131082
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181028
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.5411496
X-RAY DIFFRACTIONr_angle_other_deg1.3381.7162378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6925124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10724.28628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77415190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.406154
X-RAY DIFFRACTIONr_chiral_restr0.0640.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02192
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_it0.9631.897478
X-RAY DIFFRACTIONr_mcbond_other0.9631.894477
X-RAY DIFFRACTIONr_mcangle_it1.552.826596
X-RAY DIFFRACTIONr_mcangle_other1.5492.829597
X-RAY DIFFRACTIONr_scbond_it1.2013.155604
X-RAY DIFFRACTIONr_scbond_other1.0893.098588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7454.674876
X-RAY DIFFRACTIONr_long_range_B_refined4.48428.6561206
X-RAY DIFFRACTIONr_long_range_B_other4.48228.6681207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1699 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 61 -
Rwork0.385 1187 -
obs--94.4 %
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)
11.09010.41450.99082.29961.89218.3415-0.0105-0.08270.0308-0.0385-0.0605-0.0519-0.01540.15470.07090.19430.00670.06220.01660.00350.0233-23.936-18.17413.97
22.8848-1.1339-3.26712.20581.76337.4030.03720.0776-0.02440.0143-0.0271-0.10680.03250.1805-0.01010.2171-0.00730.02870.023-0.00330.0124-23.935-16.8315.457
35.06630.10747.81471.1156-0.477712.61880.25-0.2448-0.27520.0755-0.0567-0.0990.1625-0.1726-0.19330.4338-0.0026-0.00040.56760.02750.6311-6.666-19.18931.697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 61
2X-RAY DIFFRACTION2B3 - 61
3X-RAY DIFFRACTION3C9 - 17

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