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- PDB-9rpl: Lactobacillus acidophilus SlpA self assembly domains I-II (aa 49-308) -

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Basic information

Entry
Database: PDB / ID: 9rpl
TitleLactobacillus acidophilus SlpA self assembly domains I-II (aa 49-308)
ComponentsS-layer protein
KeywordsSTRUCTURAL PROTEIN / Surface layer / self assembly / Lactobacillus
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
FORMIC ACID / S-layer protein
Similarity search - Component
Biological speciesLactobacillus acidophilus NCFM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsGrininger, C. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundDOC 130 Austria
CitationJournal: Protein Sci. / Year: 2026
Title: Guiding AlphaFold predictions with experimental knowledge to inform dynamics and interactions with VAIRO.
Authors: Trivino, J. / Jimenez, E. / Grininger, C. / Caballero, I. / Medina, A. / Castellvi, A. / Petrillo, G. / Govantes, F. / Sagmeister, T. / Alcorlo, M. / Hermoso, J.A. / Sammito, M.D. / ...Authors: Trivino, J. / Jimenez, E. / Grininger, C. / Caballero, I. / Medina, A. / Castellvi, A. / Petrillo, G. / Govantes, F. / Sagmeister, T. / Alcorlo, M. / Hermoso, J.A. / Sammito, M.D. / Diederichs, K. / Pavkov-Keller, T. / Uson, I.
History
DepositionJun 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer protein
B: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3237
Polymers56,0012
Non-polymers3225
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-10 kcal/mol
Surface area28150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.069, 50.559, 118.638
Angle α, β, γ (deg.)90.000, 113.940, 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

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Components

#1: Protein S-layer protein / Surface layer protein / SA-protein


Mass: 28000.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus NCFM (bacteria)
Gene: slpA, LBA0169 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35829
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 3350, 50 mM sodium formate, 150 mM trisodiumcitrate; 4 g/l protein solution in 25 mM HEPES pH 7.5, 150 mM NaCl; 0.3 ul condition + 0.3 ul protein solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.929→68.125 Å / Num. obs: 37108 / % possible obs: 92.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.61 Å2 / CC1/2: 0.987 / Net I/σ(I): 8.3
Reflection shellResolution: 1.929→2.164 Å / Num. unique obs: 1855 / CC1/2: 0.697

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.1.7data reduction
STARANISO2.4.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→54.22 Å / SU ML: 0.2155 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.72
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2432 1838 4.95 %
Rwork0.2042 35265 -
obs0.2061 37103 60.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.92 Å2
Refinement stepCycle: LAST / Resolution: 1.93→54.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 21 260 4068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383854
X-RAY DIFFRACTIONf_angle_d0.62765274
X-RAY DIFFRACTIONf_chiral_restr0.0518670
X-RAY DIFFRACTIONf_plane_restr0.0035690
X-RAY DIFFRACTIONf_dihedral_angle_d5.5884547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.778980.3439155X-RAY DIFFRACTION3.5
1.98-2.040.3448150.311393X-RAY DIFFRACTION8.73
2.04-2.110.3263260.2746570X-RAY DIFFRACTION12.78
2.11-2.180.3243410.2822881X-RAY DIFFRACTION19.76
2.18-2.270.3444860.27461351X-RAY DIFFRACTION30.83
2.27-2.370.30071200.2882423X-RAY DIFFRACTION53.92
2.37-2.50.26431980.29573274X-RAY DIFFRACTION74.33
2.5-2.650.27681990.28363980X-RAY DIFFRACTION88.39
2.65-2.860.34642500.28354396X-RAY DIFFRACTION99.1
2.86-3.140.26041970.23254382X-RAY DIFFRACTION96.58
3.14-3.60.27082300.20614280X-RAY DIFFRACTION95.27
3.6-4.530.1942210.15374524X-RAY DIFFRACTION100
4.54-54.220.18192470.14584656X-RAY DIFFRACTION99.88

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