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- PDB-7qfl: Crystal structure of S-layer protein SlpA from Lactobacillus acid... -

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Basic information

Entry
Database: PDB / ID: 7qfl
TitleCrystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain II (aa 199-308)
ComponentsS-layer protein
KeywordsSTRUCTURAL PROTEIN / s-layer / surface layer / bacterial / lactobacillus acidophilus / SlpA / self-assembly
Function / homology
Function and homology information


structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / extracellular region
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
ACETATE ION / PHOSPHATE ION / S-layer protein
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSagmeister, T. / Dordic, A. / Eder, E. / 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 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3133
Polymers14,1591
Non-polymers1542
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-3 kcal/mol
Surface area6310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.851, 55.851, 63.732
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-576-

HOH

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Components

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


Mass: 14158.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: slpA, LBA0169 / Production host: Escherichia coli (E. coli) / References: UniProt: P35829
#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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: protein stock solution of 18.5 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 1-1 (0.18 M lithium sulfate, 90 mM sodium acetate pH 4.5 and 45 % w/v PEG 400) with protein ...Details: protein stock solution of 18.5 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 1-1 (0.18 M lithium sulfate, 90 mM sodium acetate pH 4.5 and 45 % w/v PEG 400) with protein end concentration of 12.3 mg/mL corresponding to 66.67 % of protein solution in the 1.5 uL drop.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→48.37 Å / Num. obs: 23163 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.042 / Rrim(I) all: 0.095 / Net I/σ(I): 13.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.85 / Num. unique obs: 21345 / CC1/2: 0.821 / Rpim(I) all: 0.427 / Rrim(I) all: 0.953

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QEC

7qec


Resolution: 1.4→48.368 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.836 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1981 1177 5.088 %
Rwork0.1702 21956 -
all0.172 --
obs-23133 99.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.361 Å2-0.181 Å2-0 Å2
2---0.361 Å20 Å2
3---1.171 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 0 9 85 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.013811
X-RAY DIFFRACTIONr_bond_other_d0.0010.016768
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.6431113
X-RAY DIFFRACTIONr_angle_other_deg1.5471.5871756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4812635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40515120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.184151
X-RAY DIFFRACTIONr_chiral_restr0.090.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02183
X-RAY DIFFRACTIONr_nbd_refined0.2080.2120
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.2635
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2386
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.242
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.29
X-RAY DIFFRACTIONr_nbd_other0.2370.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.213
X-RAY DIFFRACTIONr_mcbond_it1.7251.724426
X-RAY DIFFRACTIONr_mcbond_other1.6431.72424
X-RAY DIFFRACTIONr_mcangle_it2.4682.578533
X-RAY DIFFRACTIONr_mcangle_other2.4722.579534
X-RAY DIFFRACTIONr_scbond_it3.5542.118385
X-RAY DIFFRACTIONr_scbond_other3.5542.119386
X-RAY DIFFRACTIONr_scangle_it5.0083.034580
X-RAY DIFFRACTIONr_scangle_other5.0043.035581
X-RAY DIFFRACTIONr_lrange_it5.60821.74827
X-RAY DIFFRACTIONr_lrange_other5.46821.345814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.226850.24616030.24616910.8870.90199.82260.217
1.436-1.4760.255970.21815250.2216220.8960.9151000.192
1.476-1.5180.23980.19315080.19616070.9210.93599.93780.164
1.518-1.5650.211690.17114830.17315520.9490.9471000.145
1.565-1.6160.17610.15814360.15814970.9630.9611000.138
1.616-1.6730.175690.16614000.16714690.9580.9611000.146
1.673-1.7360.197880.15813300.1614180.9590.9621000.141
1.736-1.8070.173530.14713060.14813590.950.9651000.137
1.807-1.8870.207520.15412430.15612960.950.96199.92280.147
1.887-1.9790.19750.15511720.15712470.9530.9651000.154
1.979-2.0860.182620.15711280.15811900.9580.9691000.159
2.086-2.2120.206570.16110840.16311410.9520.9641000.168
2.212-2.3650.176720.14910030.1510750.9570.9691000.16
2.365-2.5540.181650.1559230.1579880.9610.9651000.169
2.554-2.7960.214340.1618890.1639230.9360.9571000.179
2.796-3.1250.183290.1678090.1678380.9610.9651000.19
3.125-3.6060.177350.177110.177460.9650.9681000.195
3.606-4.4110.135310.1636160.1626470.9740.971000.2
4.411-6.2120.318200.2074940.215140.940.9631000.246
6.212-48.3680.271250.2352850.2383100.9540.9441000.312

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