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- PDB-8alu: Crystal structure of the teichoic acid binding domain of SlpA, S-... -

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Basic information

Entry
Database: PDB / ID: 8alu
TitleCrystal structure of the teichoic acid binding domain of SlpA, S-layer protein from Lactobacillus acidophilus (aa. 314-444)
ComponentsS-layer protein
KeywordsCELL ADHESION / s-layer / surface layer / cell wall binding / teichoic acids
Function / homologyLactobacillus surface layer protein / Surface layer protein A domain / Surface layer protein A domain / structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / extracellular region / PHOSPHATE ION / S-layer protein
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsEder, M. / Dordic, A. / Sagmeister, T. / Vejzovic, D. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29432 Austria
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: The molecular architecture of Lactobacillus S-layer: Assembly and attachment to teichoic acids.
Authors: Sagmeister, T. / Gubensak, N. / Buhlheller, C. / Grininger, C. / Eder, M. / Ðordic, A. / Millan, C. / Medina, A. / Murcia, P.A.S. / Berni, F. / Hynonen, U. / Vejzovic, D. / Damisch, E. ...Authors: Sagmeister, T. / Gubensak, N. / Buhlheller, C. / Grininger, C. / Eder, M. / Ðordic, A. / Millan, C. / Medina, A. / Murcia, P.A.S. / Berni, F. / Hynonen, U. / Vejzovic, D. / Damisch, E. / Kulminskaya, N. / Petrowitsch, L. / Oberer, M. / Palva, A. / Malanovic, N. / Codee, J. / Keller, W. / Uson, I. / Pavkov-Keller, T.
History
DepositionAug 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 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 / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0183
Polymers14,8281
Non-polymers1902
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-14 kcal/mol
Surface area7720 Å2
Unit cell
Length a, b, c (Å)80.430, 27.050, 61.890
Angle α, β, γ (deg.)90.000, 91.046, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

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Components

#1: Protein S-layer protein


Mass: 14827.815 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: CXB72_00965 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A809K9V2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Index screen condition #80 (0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25 % PEG 3350) with a protein stock solution of 20 mg/mL in 20 mM ADA pH 6.5 and 100 mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.09→40.21 Å / Num. obs: 12330 / % possible obs: 84.51 % / Redundancy: 2.9 % / Biso Wilson estimate: 35.99 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.031 / Rrim(I) all: 0.056 / Net I/σ(I): 15.46
Reflection shellResolution: 2.09→2.17 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 340 / CC1/2: 0.751 / Rpim(I) all: 0.418 / Rrim(I) all: 0.7 / % possible all: 44

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.16_3549refinement
PHENIXphasing
Cootmodel building
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QEH

7qeh


Resolution: 2.09→40.21 Å / SU ML: 0.3115 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.6413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2597 1228 9.96 %
Rwork0.2079 11102 -
obs0.2133 12330 80.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.63 Å2
Refinement stepCycle: LAST / Resolution: 2.09→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 10 45 1100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171071
X-RAY DIFFRACTIONf_angle_d0.39751444
X-RAY DIFFRACTIONf_chiral_restr0.0449159
X-RAY DIFFRACTIONf_plane_restr0.0014178
X-RAY DIFFRACTIONf_dihedral_angle_d2.2878640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.180.3721610.3286605X-RAY DIFFRACTION39.22
2.18-2.280.3839850.3045796X-RAY DIFFRACTION51.4
2.28-2.40.29911150.26391066X-RAY DIFFRACTION69.68
2.4-2.550.31051650.261418X-RAY DIFFRACTION92.84
2.55-2.740.28761700.28181437X-RAY DIFFRACTION94.03
2.74-3.020.29781630.23831485X-RAY DIFFRACTION94.17
3.02-3.460.28531510.20971433X-RAY DIFFRACTION95.08
3.46-4.350.22341680.17731459X-RAY DIFFRACTION94.98
4.35-40.210.21651500.15961403X-RAY DIFFRACTION91.09

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