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- PDB-7aed: VirB8 domain of PrgL from Enterococcus faecalis pCF10 -

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Basic information

Entry
Database: PDB / ID: 7aed
TitleVirB8 domain of PrgL from Enterococcus faecalis pCF10
ComponentsPrgL
KeywordsMEMBRANE PROTEIN / conjugation / T4SS / VirB8
Function / homologymembrane / PrgL
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / SAD / Resolution: 1.753 Å
AuthorsJaeger, F. / Berntsson, R.P.A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Wenner-Gren FoundationUPD2018-0008 Sweden
Swedish Research Council2016- 03599 Sweden
Citation
Journal: Structure / Year: 2022
Title: Structure of the enterococcal T4SS protein PrgL reveals unique dimerization interface in the VirB8 protein family.
Authors: Jager, F. / Lamy, A. / Sun, W.S. / Guerini, N. / Berntsson, R.P.
#1: Journal: Biorxiv / Year: 2020
Title: Structure of the enterococcal T4SS protein PrgL reveals unique dimerization interface in the VirB8 protein family
Authors: Jaeger, F. / Lamy, A. / Guerini, N. / Sun, W.S. / Berntsson, R.P.A.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PrgL
B: PrgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5014
Polymers45,0822
Non-polymers4182
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint9 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.521, 124.521, 66.426
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein PrgL


Mass: 22541.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: prgL / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: D1LHF8
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: bis-Tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.753→41.86 Å / Num. obs: 76794 / % possible obs: 99.6 % / Redundancy: 5.3 % / CC1/2: 0.99 / Rrim(I) all: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 1.753→1.86 Å / Num. unique obs: 12242 / CC1/2: 0.51

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.15.2-3472refinement
XDSdata reduction
SCALEPACKdata scaling
SOLVEphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.753→34.74 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 2033 5.29 %
Rwork0.179 36428 -
obs0.18 38461 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.44 Å2 / Biso mean: 45.4746 Å2 / Biso min: 24.75 Å2
Refinement stepCycle: final / Resolution: 1.753→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 28 155 2344
Biso mean--51.65 46.85 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.753-1.79350.29931470.283234797
1.7935-1.83830.30541300.25772450100
1.8383-1.8880.25311340.23822417100
1.888-1.94360.2411430.222420100
1.9436-2.00630.24251180.21062445100
2.0063-2.0780.21231480.20412455100
2.078-2.16120.24211170.19272415100
2.1612-2.25950.22551430.18742419100
2.2595-2.37860.21161610.19422413100
2.3786-2.52760.25231300.20322448100
2.5276-2.72270.22711230.20532448100
2.7227-2.99660.22581330.20392448100
2.9966-3.42990.21421180.19732455100
3.4299-4.320.17191520.15912404100
4.32-34.740.15231360.13692444100

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