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- PDB-7acv: SLPL/HID (LMW SLP complex with HMW SLP interacting domain - HID) ... -

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Basic information

Entry
Database: PDB / ID: 7acv
TitleSLPL/HID (LMW SLP complex with HMW SLP interacting domain - HID) from C. difficile (R7404 strain)
Components
  • HID - interacting domain of SLP HMW
  • LMW SLP
KeywordsSTRUCTURAL PROTEIN / bacterial surface layer protein / SLP LMW / SLP HMW interacting domain (HID)
Function / homologyLow molecular weight S layer protein, N-terminal / Low molecular weight S layer protein, N-terminal, subdomain / Low molecular weight S layer protein N terminal / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / N-acetylmuramoyl-L-alanine amidase activity / S-layer protein
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBarwinska-Sendra, A. / Lanzoni-Mangutchi, P. / Salgado, P.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust204877/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structure and assembly of the S-layer in C. difficile.
Authors: Paola Lanzoni-Mangutchi / Oishik Banerji / Jason Wilson / Anna Barwinska-Sendra / Joseph A Kirk / Filipa Vaz / Shauna O'Beirne / Arnaud Baslé / Kamel El Omari / Armin Wagner / Neil F ...Authors: Paola Lanzoni-Mangutchi / Oishik Banerji / Jason Wilson / Anna Barwinska-Sendra / Joseph A Kirk / Filipa Vaz / Shauna O'Beirne / Arnaud Baslé / Kamel El Omari / Armin Wagner / Neil F Fairweather / Gillian R Douce / Per A Bullough / Robert P Fagan / Paula S Salgado /
Abstract: Many bacteria and archaea possess a two-dimensional protein array, or S-layer, that covers the cell surface and plays crucial roles in cell physiology. Here, we report the crystal structure of SlpA, ...Many bacteria and archaea possess a two-dimensional protein array, or S-layer, that covers the cell surface and plays crucial roles in cell physiology. Here, we report the crystal structure of SlpA, the main S-layer protein of the bacterial pathogen Clostridioides difficile, and use electron microscopy to study S-layer organisation and assembly. The SlpA crystal lattice mimics S-layer assembly in the cell, through tiling of triangular prisms above the cell wall, interlocked by distinct ridges facing the environment. Strikingly, the array is very compact, with pores of only ~10 Å in diameter, compared to other S-layers (30-100 Å). The surface-exposed flexible ridges are partially dispensable for overall structure and assembly, although a mutant lacking this region becomes susceptible to lysozyme, an important molecule in host defence. Thus, our work gives insights into S-layer organisation and provides a basis for development of C. difficile-specific therapeutics.
History
DepositionSep 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LMW SLP
B: LMW SLP
C: HID - interacting domain of SLP HMW


Theoretical massNumber of molelcules
Total (without water)73,8103
Polymers73,8103
Non-polymers00
Water2,990166
1
A: LMW SLP
C: HID - interacting domain of SLP HMW


Theoretical massNumber of molelcules
Total (without water)39,7882
Polymers39,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-21 kcal/mol
Surface area18200 Å2
MethodPISA
2
B: LMW SLP


Theoretical massNumber of molelcules
Total (without water)34,0221
Polymers34,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.870, 29.446, 144.329
Angle α, β, γ (deg.)90.000, 94.219, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein LMW SLP / S-layer protein


Mass: 34021.891 Da / Num. of mol.: 2 / Fragment: LMW SLP from C. difficile S-layer
Source method: isolated from a genetically manipulated source
Details: RT017, SLCT7b / Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: slpA, SAMEA708418_00075 / Variant: R7404 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9AEM2, N-acetylmuramoyl-L-alanine amidase
#2: Protein/peptide HID - interacting domain of SLP HMW / S-layer protein


Mass: 5766.458 Da / Num. of mol.: 1
Fragment: HID - Interacting domain of HMW SLP (SLPH) from C. difficile S-layer
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: slpA, SAMEA708418_00075 / Variant: R7404 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9AEM2, N-acetylmuramoyl-L-alanine amidase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Compound detailsChain B could not be fully traced in the electron density maps, with considerable regions beyond ...Chain B could not be fully traced in the electron density maps, with considerable regions beyond residue 110 not modelled.

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulphate, 0.1 M MES pH6.5, 35 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.4→86.35 Å / Num. obs: 29460 / % possible obs: 99.54 % / Redundancy: 5.1 % / Biso Wilson estimate: 34.87 Å2 / CC1/2: 0.979 / Net I/σ(I): 5.48
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2924 / CC1/2: 0.713

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CVZ, D_1292110990

3cvz


Resolution: 2.4→86.2 Å / SU ML: 0.4131 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.9679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3012 1391 4.74 %RANDOM
Rwork0.2512 27939 --
obs0.2535 29330 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→86.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 0 166 3643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323513
X-RAY DIFFRACTIONf_angle_d0.57124750
X-RAY DIFFRACTIONf_chiral_restr0.0461572
X-RAY DIFFRACTIONf_plane_restr0.0032603
X-RAY DIFFRACTIONf_dihedral_angle_d5.2154482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.34911580.30162766X-RAY DIFFRACTION99.76
2.49-2.590.34741390.27262707X-RAY DIFFRACTION99.34
2.59-2.70.38911400.27542774X-RAY DIFFRACTION99.49
2.7-2.850.32181390.27282718X-RAY DIFFRACTION99.34
2.85-3.020.33231360.27262778X-RAY DIFFRACTION99.69
3.02-3.260.32531430.26722804X-RAY DIFFRACTION99.56
3.26-3.590.29031270.23492756X-RAY DIFFRACTION99.45
3.59-4.10.2591160.22472840X-RAY DIFFRACTION99.86
4.1-5.170.26181330.21652837X-RAY DIFFRACTION99.53
5.17-86.20.29261600.26982959X-RAY DIFFRACTION99.27

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