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- PDB-8onb: Structure of the C-terminal beta helix domain of the Bdellovibrio... -

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Basic information

Entry
Database: PDB / ID: 8onb
TitleStructure of the C-terminal beta helix domain of the Bdellovibrio bacteriovorus Bd3182 fibre
ComponentsCell wall surface anchor family protein
KeywordsCELL ADHESION / Fibre / adhesin
Function / homology: / Chaperone of endosialidase / Intramolecular chaperone auto-processing domain / Intramolecular chaperone auto-processing (ICA) domain profile. / protein autoprocessing / sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / Cell wall surface anchor family protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsCaulton, S.G. / Lovering, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209437/Z/17/Z United Kingdom
CitationJournal: Nat Microbiol / Year: 2024
Title: Bdellovibrio bacteriovorus uses chimeric fibre proteins to recognize and invade a broad range of bacterial hosts.
Authors: Caulton, S.G. / Lambert, C. / Tyson, J. / Radford, P. / Al-Bayati, A. / Greenwood, S. / Banks, E.J. / Clark, C. / Till, R. / Pires, E. / Sockett, R.E. / Lovering, A.L.
History
DepositionApr 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 26, 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

Downloads & links

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Assembly

Deposited unit
A: Cell wall surface anchor family protein
B: Cell wall surface anchor family protein
C: Cell wall surface anchor family protein
D: Cell wall surface anchor family protein
E: Cell wall surface anchor family protein
F: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)93,1146
Polymers93,1146
Non-polymers00
Water11,295627
1
A: Cell wall surface anchor family protein
B: Cell wall surface anchor family protein
C: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)46,5573
Polymers46,5573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16580 Å2
ΔGint-87 kcal/mol
Surface area11430 Å2
2
D: Cell wall surface anchor family protein
E: Cell wall surface anchor family protein
F: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)46,5573
Polymers46,5573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16690 Å2
ΔGint-85 kcal/mol
Surface area11930 Å2
Unit cell
Length a, b, c (Å)86.561, 48.397, 92.964
Angle α, β, γ (deg.)90.00, 102.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cell wall surface anchor family protein


Mass: 15519.053 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd3182 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MIH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium acetate tetrahydrate, 0.1 M MES pH 6.5, 10 % w/v PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.12→84.35 Å / Num. obs: 176672 / % possible obs: 61.3 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 16.4
Reflection shellResolution: 1.12→1.241 Å / Num. unique obs: 8836 / CC1/2: 0.706

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→84.35 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1723 8753 4.95 %
Rwork0.1488 --
obs0.15 176660 61.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.12→84.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5204 0 0 627 5831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.189
X-RAY DIFFRACTIONf_dihedral_angle_d9.6731847
X-RAY DIFFRACTIONf_chiral_restr0.102918
X-RAY DIFFRACTIONf_plane_restr0.009986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.1201120.2508193X-RAY DIFFRACTION2
1.13-1.150.3248200.2454422X-RAY DIFFRACTION5
1.15-1.160.2984310.2366798X-RAY DIFFRACTION9
1.16-1.170.2733510.2192968X-RAY DIFFRACTION11
1.17-1.190.2394670.22141126X-RAY DIFFRACTION13
1.19-1.210.2065760.22591393X-RAY DIFFRACTION15
1.21-1.220.2306800.20681645X-RAY DIFFRACTION18
1.22-1.240.2351090.20321909X-RAY DIFFRACTION21
1.24-1.260.22461100.21692211X-RAY DIFFRACTION24
1.26-1.280.21581390.20822539X-RAY DIFFRACTION28
1.28-1.30.21331690.1912991X-RAY DIFFRACTION33
1.3-1.330.22221880.19153763X-RAY DIFFRACTION41
1.33-1.350.23582160.19324444X-RAY DIFFRACTION49
1.35-1.380.23092850.19225426X-RAY DIFFRACTION60
1.38-1.410.22223570.196681X-RAY DIFFRACTION74
1.41-1.440.20814090.18677827X-RAY DIFFRACTION86
1.44-1.480.20944240.17318512X-RAY DIFFRACTION93
1.48-1.520.19454760.16548825X-RAY DIFFRACTION97
1.52-1.560.19494720.15098973X-RAY DIFFRACTION98
1.56-1.620.1684520.14258951X-RAY DIFFRACTION98
1.62-1.670.17824870.1429015X-RAY DIFFRACTION99
1.67-1.740.16874590.13769060X-RAY DIFFRACTION99
1.74-1.820.15094990.13469018X-RAY DIFFRACTION99
1.82-1.920.15084760.13689051X-RAY DIFFRACTION99
1.92-2.040.16274110.12819181X-RAY DIFFRACTION99
2.04-2.190.16053810.13047757X-RAY DIFFRACTION85
2.19-2.410.15664180.13448116X-RAY DIFFRACTION88
2.41-2.760.17814870.15039183X-RAY DIFFRACTION100
2.76-3.480.174750.1468870X-RAY DIFFRACTION96
3.48-84.350.16745170.15619059X-RAY DIFFRACTION96

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