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- PDB-8bz2: Crystal structure of outer membrane attachment porin OmpM1 SLH domain -

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Basic information

Entry
Database: PDB / ID: 8bz2
TitleCrystal structure of outer membrane attachment porin OmpM1 SLH domain
ComponentsS-layer homology domain-containing protein
KeywordsSTRUCTURAL PROTEIN / Outer membrane attachment / peptidoglycan-binding
Function / homology: / S-layer / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / S-layer homology domain-containing protein
Function and homology information
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.7 Å
AuthorsSilale, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes.
Authors: Augustinas Silale / Yiling Zhu / Jerzy Witwinowski / Robert E Smith / Kahlan E Newman / Satya P Bhamidimarri / Arnaud Baslé / Syma Khalid / Christophe Beloin / Simonetta Gribaldo / Bert van den Berg /
Abstract: The outer membrane (OM) in diderm, or Gram-negative, bacteria must be tethered to peptidoglycan for mechanical stability and to maintain cell morphology. Most diderm phyla from the Terrabacteria ...The outer membrane (OM) in diderm, or Gram-negative, bacteria must be tethered to peptidoglycan for mechanical stability and to maintain cell morphology. Most diderm phyla from the Terrabacteria group have recently been shown to lack well-characterised OM attachment systems, but instead have OmpM, which could represent an ancestral tethering system in bacteria. Here, we have determined the structure of the most abundant OmpM protein from Veillonella parvula (diderm Firmicutes) by single particle cryogenic electron microscopy. We also characterised the channel properties of the transmembrane β-barrel of OmpM and investigated the structure and PG-binding properties of its periplasmic stalk region. Our results show that OM tethering and nutrient acquisition are genetically linked in V. parvula, and probably other diderm Terrabacteria. This dual function of OmpM may have played a role in the loss of the OM in ancestral bacteria and the emergence of monoderm bacterial lineages.
History
DepositionDec 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: S-layer homology domain-containing protein
B: S-layer homology domain-containing protein
C: S-layer homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4026
Polymers32,1143
Non-polymers2883
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-28 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.710, 118.710, 47.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11C-201-

SO4

21C-202-

SO4

31C-202-

SO4

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Components

#1: Protein S-layer homology domain-containing protein


Mass: 10704.768 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: SKV38
Gene: D3219_09385, DWV36_08570, FNLLGLLA_01389, GL281_07935, HMPREF1865_01844
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A100YN03
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M citric acid pH 3.5 2.0 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8984 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8984 Å / Relative weight: 1
ReflectionResolution: 1.57→34.78 Å / Num. obs: 34489 / % possible obs: 99.5 % / Redundancy: 9 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.017 / Net I/σ(I): 17.1
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1590 / CC1/2: 0.23 / Rpim(I) all: 0.884 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.7→34.78 Å / SU ML: 0.2792 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 33.2812
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 1245 4.56 %
Rwork0.2239 26065 -
obs0.225 27310 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 15 82 2000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01081963
X-RAY DIFFRACTIONf_angle_d1.21892669
X-RAY DIFFRACTIONf_chiral_restr0.066281
X-RAY DIFFRACTIONf_plane_restr0.0089371
X-RAY DIFFRACTIONf_dihedral_angle_d14.4325716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.39161630.3432883X-RAY DIFFRACTION100
1.77-1.850.33091460.28722905X-RAY DIFFRACTION100
1.85-1.950.34491270.2672889X-RAY DIFFRACTION99.97
1.95-2.070.26791510.24632895X-RAY DIFFRACTION100
2.07-2.230.29341490.2472864X-RAY DIFFRACTION100
2.23-2.450.2661080.25382929X-RAY DIFFRACTION100
2.45-2.810.30271430.2612891X-RAY DIFFRACTION100
2.81-3.540.24191110.2362921X-RAY DIFFRACTION100
3.54-34.780.20581470.17762888X-RAY DIFFRACTION99.93

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