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- PDB-7qec: Crystal structure of SlpA - domain II, domain that is involved in... -

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Basic information

Entry
Database: PDB / ID: 7qec
TitleCrystal structure of SlpA - domain II, domain that is involved in the self-assembly of the S-layer from Lactobacillus amylovorus
ComponentsS-layer
KeywordsSTRUCTURAL PROTEIN / s-layer / self-assembly / lactobacillus amylovorus
Function / homology
Function and homology information


structural constituent of cell wall / S-layer / peptidoglycan-based cell wall
Similarity search - Function
: / : / SlpA N-terminal domain / SlpA domain II / Lactobacillus surface layer protein / Surface layer protein A domain / Surface layer protein A domain
Similarity search - Domain/homology
Biological speciesLactobacillus amylovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.95 Å
AuthorsEder, M. / Dordic, A. / Millan, C. / Sagmeister, T. / Uson, I. / 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
DepositionDec 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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


Theoretical massNumber of molelcules
Total (without water)11,6421
Polymers11,6421
Non-polymers00
Water81145
1
A: S-layer

A: S-layer


Theoretical massNumber of molelcules
Total (without water)23,2842
Polymers23,2842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1770 Å2
ΔGint-6 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.633, 38.633, 142.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-413-

HOH

31A-443-

HOH

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Components

#1: Protein S-layer


Mass: 11641.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus amylovorus (strain GRL 1112) (bacteria)
Strain: GRL 1112 / Gene: LA2_00970 / Production host: Escherichia coli (E. coli) / References: UniProt: E4SK47
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus screen condition #1-24 (30 mM of each halogen (sodium fluoride, sodium bromide and sodium iodide), 0.1 M Bicine/Trizma base pH 8.5 with 12.5% v/v MPD, 12.5 % PEG 1000 and 12.5 % w/v ...Details: Morpheus screen condition #1-24 (30 mM of each halogen (sodium fluoride, sodium bromide and sodium iodide), 0.1 M Bicine/Trizma base pH 8.5 with 12.5% v/v MPD, 12.5 % PEG 1000 and 12.5 % w/v PEG 3350). Protein stock solution of 4.18 mg/mL in 10 mM Hepes pH 7 and 50 mM NaCl. Drops: 0.5 + 0.5uL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.95→35.61 Å / Num. obs: 14655 / % possible obs: 98.13 % / Redundancy: 18.9 % / Biso Wilson estimate: 33.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.026 / Rrim(I) all: 0.118 / Net I/σ(I): 17.79
Reflection shellResolution: 1.951→2.021 Å / Rmerge(I) obs: 0.9 / Num. unique obs: 682 / CC1/2: 0.759 / Rpim(I) all: 0.244

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Arcimboldophasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.95→35.61 Å / SU ML: 0.2341 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 1469 10.02 %
Rwork0.1846 13185 -
obs0.1903 14654 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.76 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 0 0 45 814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008786
X-RAY DIFFRACTIONf_angle_d0.77891072
X-RAY DIFFRACTIONf_chiral_restr0.0589135
X-RAY DIFFRACTIONf_plane_restr0.0051139
X-RAY DIFFRACTIONf_dihedral_angle_d2.7136628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.26171180.23111065X-RAY DIFFRACTION78.4
2.02-2.10.28291490.2311347X-RAY DIFFRACTION100
2.1-2.20.34031440.21211321X-RAY DIFFRACTION99.86
2.2-2.310.23111580.2071361X-RAY DIFFRACTION99.93
2.31-2.460.25931450.20221355X-RAY DIFFRACTION100
2.46-2.650.2681540.19211324X-RAY DIFFRACTION100
2.65-2.910.22111490.18371355X-RAY DIFFRACTION99.93
2.91-3.340.25261480.1811358X-RAY DIFFRACTION100
3.34-4.20.19441580.17361353X-RAY DIFFRACTION100
4.2-35.610.26011460.16951346X-RAY DIFFRACTION100

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