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- PDB-7qeh: LTA-binding domain of SlpA, the S-layer protein from Lactobacillu... -

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Basic information

Entry
Database: PDB / ID: 7qeh
TitleLTA-binding domain of SlpA, the S-layer protein from Lactobacillus amylovorus
ComponentsS-layer
KeywordsCELL ADHESION / s-layer / LTA-binding / lactobacillus amylovorus / polymer binding
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
PHOSPHATE ION / S-layer
Similarity search - Component
Biological speciesLactobacillus amylovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å
AuthorsEder, M. / Dordic, A. / Sagmeister, T. / 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 3, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-layer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3272
Polymers16,2321
Non-polymers951
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.561, 43.481, 89.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein S-layer


Mass: 16231.854 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus screen condition #2-29 (20 mM of each carboxylic acid (sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate, and sodium ...Details: Morpheus screen condition #2-29 (20 mM of each carboxylic acid (sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate, and sodium oxamate), 0.1 M sodium HEPES- MOPS pH 7.5 with 20 % v/v PEG 500 MME and 10 % w/v PEG 20000). A protein stock solution of 20 mg/mL in 10 mM HEPES pH 7 and 100 mM NaCl was used. 1uL drop with 1:1 ration protein to reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.67→39.08 Å / Num. obs: 26186 / % possible obs: 99.39 % / Redundancy: 12.2 % / Biso Wilson estimate: 18.71 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.032 / Rrim(I) all: 0.114 / Net I/σ(I): 19.84
Reflection shellResolution: 1.67→1.734 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1361 / CC1/2: 0.805 / CC star: 0.947 / Rpim(I) all: 0.316

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXCDphasing
SHELXEmodel building
PHENIX1.16_3549refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.67→39.08 Å / SU ML: 0.1598 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1904 2612 9.98 %
Rwork0.1626 23573 -
obs0.1655 26185 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.47 Å2
Refinement stepCycle: LAST / Resolution: 1.67→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 5 75 1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091994
X-RAY DIFFRACTIONf_angle_d0.99831336
X-RAY DIFFRACTIONf_chiral_restr0.0666150
X-RAY DIFFRACTIONf_plane_restr0.0056164
X-RAY DIFFRACTIONf_dihedral_angle_d12.928603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.27561230.27521079X-RAY DIFFRACTION85.31
1.71-1.740.20841430.19921235X-RAY DIFFRACTION99.93
1.74-1.770.23591360.19111253X-RAY DIFFRACTION99.86
1.77-1.810.22631410.17521236X-RAY DIFFRACTION99.78
1.81-1.850.24541350.17551237X-RAY DIFFRACTION100
1.85-1.90.21971450.16611273X-RAY DIFFRACTION100
1.9-1.950.24291330.15961231X-RAY DIFFRACTION100
1.95-2.010.16841420.16271263X-RAY DIFFRACTION100
2.01-2.070.18021310.14791266X-RAY DIFFRACTION100
2.07-2.150.24611340.16451247X-RAY DIFFRACTION99.93
2.15-2.230.1881350.14761249X-RAY DIFFRACTION99.93
2.23-2.340.18251400.16031259X-RAY DIFFRACTION100
2.34-2.460.2031420.15871233X-RAY DIFFRACTION100
2.46-2.610.19851380.17661254X-RAY DIFFRACTION100
2.61-2.810.18851410.16911265X-RAY DIFFRACTION100
2.81-3.10.19111400.17161255X-RAY DIFFRACTION100
3.1-3.550.18161300.15041241X-RAY DIFFRACTION99.71
3.55-4.470.15591410.1411264X-RAY DIFFRACTION99.93
4.47-39.080.17831420.16761233X-RAY DIFFRACTION100

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