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- PDB-8s80: Domains 4 and 5 of Sap S-layer protein from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 8s80
TitleDomains 4 and 5 of Sap S-layer protein from Bacillus anthracis
ComponentsS-layer protein sap
KeywordsSTRUCTURAL PROTEIN / S-layer / Sap / anthracis / anthrax
Function / homology
Function and homology information


S-layer / extracellular region
Similarity search - Function
SbsA, Ig-like domain / Bacterial Ig-like domain / : / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsSogues, A. / Remaut, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 709-2021European Union
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Architecture of the Sap S-layer of revealed by integrative structural biology.
Authors: Adrià Sogues / Kendra Leigh / Ethan V Halingstad / Sander E Van der Verren / Adam J Cecil / Antonella Fioravanti / Alexander J Pak / Misha Kudryashev / Han Remaut /
Abstract: is a spore-forming gram-positive bacterium responsible for anthrax, an infectious disease with a high mortality rate and a target of concern due to bioterrorism and long-term site contamination. The ... is a spore-forming gram-positive bacterium responsible for anthrax, an infectious disease with a high mortality rate and a target of concern due to bioterrorism and long-term site contamination. The entire surface of vegetative cells in exponential or stationary growth phase is covered in proteinaceous arrays called S-layers, composed of Sap or EA1 protein, respectively. The Sap S-layer represents an important virulence factor and cell envelope support structure whose paracrystalline nature is essential for its function. However, the spatial organization of Sap in its lattice state remains elusive. Here, we employed cryoelectron tomography and subtomogram averaging to obtain a map of the Sap S-layer from tubular polymers that revealed a conformational switch between the postassembly protomers and the previously available X-ray structure of the condensed monomers. To build and validate an atomic model of the lattice within this map, we used a combination of molecular dynamics simulations, X-ray crystallography, cross-linking mass spectrometry, and biophysics in an integrative structural biology approach. The Sap lattice model produced recapitulates a close-to-physiological arrangement, reveals high-resolution details of lattice contacts, and sheds light on the mechanisms underlying the stability of the Sap layer.
History
DepositionMar 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-layer protein sap
B: S-layer protein sap
C: S-layer protein sap
F: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)95,6774
Polymers95,6774
Non-polymers00
Water1,62190
1
A: S-layer protein sap

F: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)47,8392
Polymers47,8392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
2
B: S-layer protein sap
C: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)47,8392
Polymers47,8392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.304, 63.539, 73.659
Angle α, β, γ (deg.)68.310, 81.610, 82.740
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
S-layer protein sap / Surface array protein / Surface layer protein


Mass: 23919.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Sap domains 4 and 5 / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sap, BA_0885, GBAA_0885, BAS0841 / Production host: Escherichia coli (E. coli) / References: UniProt: P49051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1M MMT (Malic Acid, MES and TRIS (1:2:2 Molar Ratio)) pH7 and 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.478→58.48 Å / Num. obs: 34369 / % possible obs: 98.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 65.77 Å2 / Rpim(I) all: 0.045 / Net I/σ(I): 9.6
Reflection shellResolution: 2.478→2.521 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1715 / CC1/2: 0.849

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→39.94 Å / SU ML: 0.3931 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 33.197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2668 2000 5.82 %
Rwork0.2198 32351 -
obs0.2226 34351 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.67 Å2
Refinement stepCycle: LAST / Resolution: 2.48→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6403 0 0 90 6493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00776461
X-RAY DIFFRACTIONf_angle_d1.00138735
X-RAY DIFFRACTIONf_chiral_restr0.05751096
X-RAY DIFFRACTIONf_plane_restr0.00471101
X-RAY DIFFRACTIONf_dihedral_angle_d5.8244879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.540.38321440.30812327X-RAY DIFFRACTION98.09
2.54-2.610.33291400.30232279X-RAY DIFFRACTION98.13
2.61-2.690.38531440.30182315X-RAY DIFFRACTION97.89
2.69-2.770.36081440.29382324X-RAY DIFFRACTION98.48
2.77-2.870.37611410.32322289X-RAY DIFFRACTION97.9
2.87-2.990.37711440.31322331X-RAY DIFFRACTION98.33
2.99-3.120.34221440.29752330X-RAY DIFFRACTION98.53
3.12-3.290.31311420.28012292X-RAY DIFFRACTION97.95
3.29-3.490.31931420.27312300X-RAY DIFFRACTION97.06
3.49-3.760.32641410.25082284X-RAY DIFFRACTION97.47
3.76-4.140.24881430.2182311X-RAY DIFFRACTION98.44
4.14-4.740.23121440.1832335X-RAY DIFFRACTION98.88
4.74-5.970.20951450.16362341X-RAY DIFFRACTION98.73
5.97-39.940.19141420.15592293X-RAY DIFFRACTION97.79
Refinement TLS params.Method: refined / Origin x: 15.5745927044 Å / Origin y: 10.4308972174 Å / Origin z: 22.6482019748 Å
111213212223313233
T0.587993448872 Å2-0.0840664392025 Å20.0181236823784 Å2-0.649402332683 Å20.0548618757564 Å2--0.505835380142 Å2
L0.546779377539 °2-0.231909066992 °20.167700884848 °2-0.626635418339 °20.251803111905 °2--0.256509601914 °2
S0.045494556206 Å °0.0816199908894 Å °0.0613512406776 Å °-0.0650730648013 Å °-0.00494193100074 Å °-0.0867225729337 Å °-0.0484477473161 Å °0.0497397707371 Å °-0.0206897780878 Å °
Refinement TLS groupSelection details: all

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