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- PDB-7acw: LID/HID (LMW SLP and HMW SLP interacting domains) from C. diffici... -

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Basic information

Entry
Database: PDB / ID: 7acw
TitleLID/HID (LMW SLP and HMW SLP interacting domains) from C. difficile (R7404 strain)
Components(S-layer protein) x 2
KeywordsSTRUCTURAL PROTEIN / Bacterial surface / S-layer
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 / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsBarwinska-Sendra, A. / Lanzoni-Mangutchi, P. / Basle, A. / 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 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer protein
B: S-layer protein
C: S-layer protein
D: S-layer protein


Theoretical massNumber of molelcules
Total (without water)28,9884
Polymers28,9884
Non-polymers00
Water1,928107
1
A: S-layer protein
B: S-layer protein


  • defined by author&software
  • Evidence: gel filtration, SLPL (SLP LMW) Interacting Domain (LID) and SLPH (SLP HMW) Interacting Domain (HID) (LIDHID) form a heterodimer. ELISA assay confirms complex formation (Fagan et al., Mol Micro, 2009)
  • 14.5 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)14,4942
Polymers14,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-22 kcal/mol
Surface area6810 Å2
MethodPISA
2
C: S-layer protein
D: S-layer protein


  • defined by author&software
  • Evidence: assay for oligomerization, SLPL (SLP LMW) Interacting Domain (LID) and SLPH (SLP HMW) Interacting Domain (HID) (LIDHID) form a heterodimer. ELISA assay confirms complex formation (Fagan et al., Mol Micro, 2009)
  • 14.5 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)14,4942
Polymers14,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-23 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.273, 56.705, 61.813
Angle α, β, γ (deg.)90.000, 122.710, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-438-

HOH

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Components

#1: Protein S-layer protein / S-layer protein


Mass: 8727.751 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RT017, SLCT7b / Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: slpA, SAMEA708418_00075 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9AEM2, N-acetylmuramoyl-L-alanine amidase
#2: Protein/peptide S-layer protein / S-layer protein


Mass: 5766.458 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RT017, SLCT7b / Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: slpA, SAMEA708418_00075 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9AEM2, N-acetylmuramoyl-L-alanine amidase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M sodium citrate tribasic dihidrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→52.01 Å / Num. obs: 34063 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.028 / Rrim(I) all: 0.055 / Net I/σ(I): 8.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Num. unique obs: 3318 / CC1/2: 0.975 / CC star: 0.994 / Rpim(I) all: 0.154 / Rrim(I) all: 0.27 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→52.01 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.506 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 1644 5 %RANDOM
Rwork0.164 ---
obs0.166 31378 96.55 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 77.08 Å2 / Biso mean: 32.518 Å2 / Biso min: 20.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å20.99 Å2
2--2.4 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: final / Resolution: 1.5→52.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 0 107 1816
Biso mean---37.89 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191737
X-RAY DIFFRACTIONr_bond_other_d0.0010.021604
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.8962347
X-RAY DIFFRACTIONr_angle_other_deg1.0782.9363751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1155210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35626.42984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92915316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.263152
X-RAY DIFFRACTIONr_chiral_restr0.0780.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021901
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.65933341
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 109 -
Rwork0.274 2172 -
all-2281 -
obs--90.59 %

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