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- PDB-7acx: H/L (SLPH/SLPL) complex from C. difficile (R7404 strain) -

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Basic information

Entry
Database: PDB / ID: 7acx
TitleH/L (SLPH/SLPL) complex 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 / S-layer protein
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLanzoni-Mangutchi, P. / Barwinska-Sendra, A. / Basle, A. / El Omari, K. / Wagner, 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 1.1Jan 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,1748
Polymers146,5394
Non-polymers6354
Water2,000111
1
A: S-layer protein
B: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5874
Polymers73,2702
Non-polymers3172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-42 kcal/mol
Surface area31830 Å2
MethodPISA
2
C: S-layer protein
D: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5874
Polymers73,2702
Non-polymers3172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-45 kcal/mol
Surface area30650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.052, 137.940, 84.734
Angle α, β, γ (deg.)90.000, 100.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 120 or resid 142...
d_2ens_1(chain "C" and (resid 3 through 315 or resid 401))
d_1ens_2chain "B"
d_2ens_2(chain "D" and (resid 1 through 219 or resid 224 through 373))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRASPA1 - 118
d_12ens_1LYSTHRA140 - 169
d_13ens_1ILETHRA185 - 313
d_14ens_1NAGNAGB
d_21ens_1THRTHRE2 - 278
d_22ens_1NAGNAGF
d_11ens_2ALAMETD1 - 369
d_21ens_2ALAGLYG1 - 219
d_22ens_2ILEMETG224 - 373

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein S-layer protein /


Mass: 33819.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Plasmid details: RT017, SLCT7b / References: UniProt: Q8KHI4
#2: Protein S-layer protein / / S-layer protein


Mass: 39450.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Plasmid details: RT017, SLCT7b
References: UniProt: Q9AEM2, N-acetylmuramoyl-L-alanine amidase
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.0M LiCl2 12% PEG 6000 0.1M MES pH6.5 10%Glyc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.65→83.26 Å / Num. obs: 51166 / % possible obs: 99.7 % / Redundancy: 48 % / Biso Wilson estimate: 57.08 Å2 / CC1/2: 0.712 / Net I/σ(I): 12
Reflection shellResolution: 2.65→2.75 Å / Num. unique obs: 5098 / CC1/2: 0.36

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CVZ, 5J6Q, D_129110990/992/995

3cvz

5j6q


Resolution: 2.65→83.26 Å / SU ML: 0.4498 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2584 5.06 %RANDOM
Rwork0.225 48443 --
obs0.228 51027 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.7 Å2
Refinement stepCycle: LAST / Resolution: 2.65→83.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9945 0 40 111 10096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007210080
X-RAY DIFFRACTIONf_angle_d1.184713650
X-RAY DIFFRACTIONf_chiral_restr0.07451659
X-RAY DIFFRACTIONf_plane_restr0.00641761
X-RAY DIFFRACTIONf_dihedral_angle_d6.06291405
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.14896918319
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS1.21932458833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.70.40561690.38952658X-RAY DIFFRACTION99.65
2.7-2.760.41041530.37292653X-RAY DIFFRACTION99.93
2.76-2.820.40151420.35952696X-RAY DIFFRACTION99.72
2.82-2.880.41351180.34352720X-RAY DIFFRACTION99.86
2.88-2.950.36941320.33452666X-RAY DIFFRACTION99.61
2.95-3.030.34511470.31092680X-RAY DIFFRACTION99.75
3.03-3.120.35031450.29552709X-RAY DIFFRACTION99.62
3.12-3.220.35451480.2862653X-RAY DIFFRACTION99.64
3.22-3.340.31311590.25552643X-RAY DIFFRACTION99.4
3.34-3.470.37271330.24232708X-RAY DIFFRACTION99.89
3.47-3.630.28151660.22972659X-RAY DIFFRACTION99.82
3.63-3.820.28841540.21822690X-RAY DIFFRACTION99.68
3.82-4.060.27211460.21472707X-RAY DIFFRACTION99.93
4.06-4.370.25321410.19042688X-RAY DIFFRACTION99.86
4.38-4.820.22111410.16562708X-RAY DIFFRACTION99.82
4.82-5.510.21641250.17282714X-RAY DIFFRACTION99.72
5.51-6.940.21661240.2022757X-RAY DIFFRACTION99.97
6.94-83.260.21491410.17732734X-RAY DIFFRACTION99.24
Refinement TLS params.Method: refined / Origin x: 30.7647871792 Å / Origin y: -13.0441228134 Å / Origin z: -31.8726173113 Å
111213212223313233
T0.389614744809 Å2-0.0655073848802 Å20.0242943982734 Å2-0.383422666647 Å20.0390608873109 Å2--0.32898543896 Å2
L0.244931797348 °2-0.00753532823263 °20.203445488664 °2-0.146384221646 °20.0288200552193 °2--0.15609137836 °2
S-0.0621979015403 Å °0.0710054611972 Å °0.0822821149018 Å °0.00626491937525 Å °-0.025651675354 Å °-0.00201976200177 Å °0.0205690424597 Å °0.0896172024112 Å °-0.0149489874217 Å °
Refinement TLS groupSelection details: all

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