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- PDB-8s83: Domains 3 and 6 of Sap S-layer protein from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 8s83
TitleDomains 3 and 6 of Sap S-layer protein from Bacillus anthracis
Components(S-layer protein sap) x 2
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: 2.07 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,5894
Polymers47,5894
Non-polymers00
Water5,567309
1
A: S-layer protein sap

D: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)23,7952
Polymers23,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
2
B: S-layer protein sap
C: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)23,7952
Polymers23,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.154, 61.010, 97.658
Angle α, β, γ (deg.)90.000, 91.500, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 385 through 396 or (resid 397...
d_2ens_1(chain "B" and (resid 385 through 468 or resid 470 through 490))
d_1ens_2(chain "C" and (resid 710 through 787 or (resid 788...
d_2ens_2(chain "D" and (resid 710 through 721 or (resid 722...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALALYSLYSAA385 - 4687 - 90
d_12ens_1THRTHRALAALAAA470 - 49092 - 112
d_21ens_1ALAALALYSLYSBB385 - 4687 - 90
d_22ens_1THRTHRALAALABB470 - 49092 - 112
d_11ens_2GLYGLYGLUGLUCC710 - 8088 - 106
d_21ens_2GLYGLYGLUGLUDD710 - 8088 - 106

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.991924139274, 0.0778838026378, 0.100103022994), (0.0693912227299, 0.993902252918, -0.0856922975099), (-0.106166662064, -0.0780539872854, -0.991280089044)3.52975891469, 13.9728058747, -49.7567787862
2given(-0.99222732772, 0.0316541009803, -0.120345120456), (0.039642534791, 0.997125125802, -0.0645751727039), (0.117955074337, -0.0688440366736, -0.990629647776)-3.58151283578, 43.2583752653, -47.7287964144

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Components

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


Mass: 12334.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sap Domain 3 / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sap, BA_0885, GBAA_0885, BAS0841 / Production host: Escherichia coli (E. coli) / References: UniProt: P49051
#2: Protein S-layer protein sap / Surface array protein / Surface layer protein


Mass: 11459.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sap Domain 6 / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sap, BA_0885, GBAA_0885, BAS0841 / Production host: Escherichia coli (E. coli) / References: UniProt: P49051
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M of sodium Hepes (pH 7.5) and 25% w/v PEG 2000 MME

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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 EIGER2 X 16M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.069→97.62 Å / Num. obs: 29030 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 39.53 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.069 / Net I/σ(I): 8.1
Reflection shellResolution: 2.069→2.104 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1491 / CC1/2: 0.336

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→51.74 Å / SU ML: 0.3029 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8103
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 1340 4.63 %
Rwork0.2011 27607 -
obs0.2037 28947 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.04 Å2
Refinement stepCycle: LAST / Resolution: 2.07→51.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 0 309 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843150
X-RAY DIFFRACTIONf_angle_d0.95694275
X-RAY DIFFRACTIONf_chiral_restr0.0972535
X-RAY DIFFRACTIONf_plane_restr0.0058543
X-RAY DIFFRACTIONf_dihedral_angle_d5.5592425
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.7530310737
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.834151507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.140.36231500.31882718X-RAY DIFFRACTION98.52
2.14-2.230.33231500.29282724X-RAY DIFFRACTION99.27
2.23-2.330.33621210.25842753X-RAY DIFFRACTION99.93
2.33-2.450.29981110.25462761X-RAY DIFFRACTION99.97
2.45-2.610.2951200.23442770X-RAY DIFFRACTION99.86
2.61-2.810.26081470.23012741X-RAY DIFFRACTION99.93
2.81-3.090.3681450.22272752X-RAY DIFFRACTION100
3.09-3.540.25431220.19652751X-RAY DIFFRACTION99.97
3.54-4.460.23861300.1672823X-RAY DIFFRACTION99.93
4.46-51.740.19151440.16472814X-RAY DIFFRACTION99.5

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