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

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Basic information

Entry
Database: PDB / ID: 8ojn
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: 2.51 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
DepositionMar 24, 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
C: Cell wall surface anchor family protein
E: Cell wall surface anchor family protein
D: Cell wall surface anchor family protein
F: Cell wall surface anchor family protein
B: Cell wall surface anchor family protein
A: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)93,1146
Polymers93,1146
Non-polymers00
Water1,38777
1
C: Cell wall surface anchor family protein
B: Cell wall surface anchor family protein
A: 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 area17470 Å2
ΔGint-95 kcal/mol
Surface area13080 Å2
2
E: Cell wall surface anchor family protein
D: 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 area17580 Å2
ΔGint-93 kcal/mol
Surface area13110 Å2
Unit cell
Length a, b, c (Å)93.219, 48.133, 95.595
Angle α, β, γ (deg.)90.000, 96.690, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 77 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulphate, 0.1 M imidazole/MES pH 6.5, 20 % v/v PEG 500 MME, 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.173→92.968 Å / Num. obs: 39829 / % possible obs: 87.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 48.12 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.1
Reflection shellResolution: 2.173→2.21 Å / Num. unique obs: 1511 / CC1/2: 0.349 / % possible all: 67.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
PHASERphasing
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→92.58 Å / SU ML: 0.2979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 1213 5.09 %
Rwork0.1935 22601 -
obs0.1962 23814 80.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.65 Å2
Refinement stepCycle: LAST / Resolution: 2.51→92.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5760 0 0 77 5837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585850
X-RAY DIFFRACTIONf_angle_d0.82077992
X-RAY DIFFRACTIONf_chiral_restr0.0673978
X-RAY DIFFRACTIONf_plane_restr0.00351026
X-RAY DIFFRACTIONf_dihedral_angle_d12.19791950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.610.3633310.2949695X-RAY DIFFRACTION22.46
2.61-2.730.3613230.2993470X-RAY DIFFRACTION15.31
2.73-2.870.30621580.27772755X-RAY DIFFRACTION90.02
2.87-3.050.30951960.2573053X-RAY DIFFRACTION99.88
3.05-3.290.32781530.24463095X-RAY DIFFRACTION99.97
3.29-3.620.27681720.20023088X-RAY DIFFRACTION99.94
3.62-4.140.26721670.17793093X-RAY DIFFRACTION99.76
4.14-5.210.18321430.13853139X-RAY DIFFRACTION99.3
5.21-92.580.19831700.18573213X-RAY DIFFRACTION99.59
Refinement TLS params.Method: refined / Origin x: -22.6026858309 Å / Origin y: -1.98938795608 Å / Origin z: -24.4999411071 Å
111213212223313233
T0.281088495915 Å20.0236732826957 Å20.00652060499492 Å2-0.210864761502 Å2-0.0253662591339 Å2--0.301317196041 Å2
L0.921953864488 °20.187660860546 °2-0.246257331658 °2-0.40511066774 °2-0.158103018143 °2--0.577704896172 °2
S-0.0189592139902 Å °0.110601693755 Å °0.00247070868093 Å °-0.0501034807181 Å °0.0312585535323 Å °-0.00456472250612 Å °0.00163422664202 Å °-0.0322024322892 Å °-0.00449390281202 Å °
Refinement TLS groupSelection details: all

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