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- PDB-7qlh: Crystal structure of S-layer protein SlpA from Lactobacillus amyl... -

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Basic information

Entry
Database: PDB / ID: 7qlh
TitleCrystal structure of S-layer protein SlpA from Lactobacillus amylovorus, domain I (aa 48-213)
ComponentsS-layer
KeywordsSTRUCTURAL PROTEIN / s-layer / surface layer / bacterial / lactobacillus amylovorus / SlpA / self-assembly
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGrininger, C. / Sagmeister, T. / Eder, E. / 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
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 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
B: S-layer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9845
Polymers37,7712
Non-polymers2133
Water1,09961
1
A: S-layer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0043
Polymers18,8861
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-layer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9812
Polymers18,8861
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.543, 91.756, 93.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-302-

NA

21A-412-

HOH

31B-426-

HOH

41B-440-

HOH

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Components

#1: Protein S-layer


Mass: 18885.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus amylovorus (bacteria) / Strain: GRL 1112 / Gene: LA2_00970
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E4SK47
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallization condition 0.1 M MES, 40 % v/v MPD, 5 % w/v PEG 8000 Protein solution 20 mg/ml in 20 mM HEPES pH 8.0, 100 mM NaCl Setup 0.5 ul crystallization condition + 0.5 ul protein solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9429 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9429 Å / Relative weight: 1
ReflectionResolution: 2.3→43.79 Å / Num. obs: 19468 / % possible obs: 99.02 % / Redundancy: 6.3 % / Biso Wilson estimate: 45.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05662 / Net I/σ(I): 19.32
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.4732 / Mean I/σ(I) obs: 4.17 / Num. unique obs: 1908 / CC1/2: 0.959

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QLE

7qle


Resolution: 2.3→43.79 Å / SU ML: 0.2691 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2831 1065 5.48 %
Rwork0.2231 18361 -
obs0.2262 19426 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 11 61 2528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292512
X-RAY DIFFRACTIONf_angle_d0.53163439
X-RAY DIFFRACTIONf_chiral_restr0.046400
X-RAY DIFFRACTIONf_plane_restr0.0032449
X-RAY DIFFRACTIONf_dihedral_angle_d4.9061343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.32571330.25542233X-RAY DIFFRACTION98.91
2.4-2.530.33431360.25782251X-RAY DIFFRACTION99.17
2.53-2.690.3321530.25222242X-RAY DIFFRACTION99.21
2.69-2.90.3071380.24792277X-RAY DIFFRACTION99.55
2.9-3.190.28291340.22782266X-RAY DIFFRACTION99.21
3.19-3.650.29171330.23292310X-RAY DIFFRACTION99.31
3.65-4.60.24231070.19662337X-RAY DIFFRACTION98.51
4.6-43.790.27291310.21772445X-RAY DIFFRACTION98.47

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