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- PDB-8beg: Structure of Ig-like domains from PrgB -

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Basic information

Entry
Database: PDB / ID: 8beg
TitleStructure of Ig-like domains from PrgB
ComponentsPrgB
KeywordsCELL ADHESION / Ig-like domians
Function / homology
Function and homology information


extracellular region / membrane / metal ion binding
Similarity search - Function
Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / KxYKxGKxW signal peptide ...Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsJarva, M. / Schmitt, A. / Berntsson, R.P.-A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
Carl Trygger FoundationCTS 18:39 Sweden
CitationJournal: Elife / Year: 2023
Title: Structural foundation for the role of enterococcal PrgB in conjugation, biofilm formation, and virulence.
Authors: Wei-Sheng Sun / Lena Lassinantti / Michael Järvå / Andreas Schmitt / Josy Ter Beek / Ronnie P-A Berntsson /
Abstract: Type 4 Secretion Systems are a main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. In Gram-positives, these secretion systems often rely on surface adhesins ...Type 4 Secretion Systems are a main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. In Gram-positives, these secretion systems often rely on surface adhesins to enhance cellular aggregation and mating-pair formation. One of the best studied adhesins is PrgB from the conjugative plasmid pCF10 of , which has been shown to play major roles in conjugation, biofilm formation, and importantly also in bacterial virulence. Since orthologs exist on a large number of conjugative plasmids in various different species, this makes PrgB a model protein for this widespread virulence factor. After characterizing the polymer adhesin domain of PrgB previously, we here report the structure for almost the entire remainder of PrgB, which reveals that PrgB contains four immunoglobulin (Ig)-like domains. Based on this new insight, we re-evaluate previously studied variants and present new in vivo data where specific domains or conserved residues have been removed. For the first time, we can show a decoupling of cellular aggregation from biofilm formation and conjugation in mutant phenotypes. Based on the presented data, we propose a new functional model to explain how PrgB mediates its different functions. We hypothesize that the Ig-like domains act as a rigid stalk that presents the polymer adhesin domain at the right distance from the cell wall.
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PrgB
B: PrgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,6914
Polymers143,6422
Non-polymers492
Water14,700816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALLS and mass phytometry suggests the protein is in a dimer/monomer equilibrium in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-23 kcal/mol
Surface area56450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.000, 87.500, 224.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PrgB


Mass: 71821.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: from the conjugative plasmid pCF10 / Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: prgB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04112
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: CaCl2, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.79→47.29 Å / Num. obs: 139448 / % possible obs: 98.6 % / Redundancy: 6.568 % / Biso Wilson estimate: 36.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.077 / Χ2: 0.812 / Net I/σ(I): 12.43 / Num. measured all: 915892
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.79-1.96.4341.8390.7713505622692209910.6091.99892.5
1.9-2.036.5080.951.613768221193211550.8771.03399.8
2.03-2.196.9320.5363.0613733819833198110.9530.57999.9
2.19-2.46.590.3274.9712009318264182230.9760.35599.8
2.4-2.696.7980.1749.1811276216611165870.9930.18999.9
2.69-3.16.5740.08718.039640314695146650.9970.09599.8
3.1-3.796.4870.0533.228124212549125230.9990.05499.8
3.79-5.356.140.03743.7660081981497850.9990.0499.7
5.35-47.296.1730.0347.6735235574457080.9990.03299.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold model

Resolution: 1.84→47.29 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 6485 4.98 %
Rwork0.2089 123634 -
obs0.2108 130119 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.32 Å2 / Biso mean: 45.0436 Å2 / Biso min: 26.56 Å2
Refinement stepCycle: final / Resolution: 1.84→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10052 0 11 816 10879
Biso mean--57.93 47.67 -
Num. residues----1299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.860.41532260.41024050427699
1.86-1.880.42732080.40134038424699
1.88-1.910.42882220.386441064328100
1.91-1.930.41332340.35344043427799
1.93-1.960.36142290.336140304259100
1.96-1.980.35692070.308640644271100
1.98-2.010.33222170.304441144331100
2.01-2.040.34891930.288640944287100
2.04-2.070.36131780.291841384316100
2.07-2.110.31742120.283140674279100
2.11-2.140.29882190.265541004319100
2.14-2.180.34512050.25154098430399
2.18-2.220.34592250.261440614286100
2.22-2.270.29592140.249140724286100
2.27-2.320.28312170.247841034320100
2.32-2.370.28431960.234841394335100
2.37-2.430.29372200.238640754295100
2.43-2.50.30822010.237641074308100
2.5-2.570.31231950.23941604355100
2.57-2.650.31642060.24841144320100
2.65-2.750.30522180.271841154333100
2.75-2.860.30682310.24841034334100
2.86-2.990.29822030.232741394342100
2.99-3.150.28982360.232941284364100
3.15-3.340.23442190.224141594378100
3.34-3.60.23352240.19641894413100
3.6-3.960.21342240.181941664390100
3.96-4.540.19122310.150841824413100
4.54-5.710.15632310.142542504481100
5.71-47.290.17772440.155844304674100

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