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

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Basic information

Entry
Database: PDB / ID: 7qfg
TitleCrystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain III (aa 309-444)
ComponentsS-layer protein
KeywordsCELL ADHESION / Surface Layer protein / SlpA / Lactobacillus acidophilus / Cell-wall binding / LTA binding
Function / homologyLactobacillus surface layer protein / Surface layer protein A domain / Surface layer protein A domain / structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / extracellular region / S-layer protein
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSagmeister, T. / Eder, M. / 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)16,9846
Polymers16,6331
Non-polymers3515
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-34 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.628, 43.943, 42.488
Angle α, β, γ (deg.)90.000, 98.824, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein S-layer protein


Mass: 16632.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: CXB72_00965 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A809K9V2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Index screen condition A9 (0.1 M BIS-TRIS pH 5.5, 3.0 M Sodium chloride) with protein end concentration of 10 mg/mL ...Details: Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Index screen condition A9 (0.1 M BIS-TRIS pH 5.5, 3.0 M Sodium chloride) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 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: 1.2543 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2543 Å / Relative weight: 1
ReflectionResolution: 1.65→41.99 Å / Num. obs: 22102 / % possible obs: 99.4 % / Redundancy: 3.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.07 / Rrim(I) all: 0.102 / Net I/σ(I): 11.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3 % / Rmerge(I) obs: 0.15 / Num. unique obs: 2193 / CC1/2: 0.951 / Rpim(I) all: 0.141 / Rrim(I) all: 0.206

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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: 7QEH

7qeh


Resolution: 1.65→41.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.315 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1836 1143 5.172 %
Rwork0.1585 20958 -
all0.16 --
obs-22101 99.321 %
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: 16.567 Å2
Baniso -1Baniso -2Baniso -3
1-0.134 Å2-0 Å2-0.092 Å2
2--0.609 Å2-0 Å2
3----0.682 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 18 197 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131121
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151087
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.671513
X-RAY DIFFRACTIONr_angle_other_deg1.4571.5992497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6122.22254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85615200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.205156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02263
X-RAY DIFFRACTIONr_nbd_refined0.2140.2150
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.2963
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2553
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.298
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.29
X-RAY DIFFRACTIONr_nbd_other0.160.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.219
X-RAY DIFFRACTIONr_mcbond_it1.541.385548
X-RAY DIFFRACTIONr_mcbond_other1.491.38547
X-RAY DIFFRACTIONr_mcangle_it2.2792.071685
X-RAY DIFFRACTIONr_mcangle_other2.2842.075686
X-RAY DIFFRACTIONr_scbond_it3.1191.742573
X-RAY DIFFRACTIONr_scbond_other3.1161.743574
X-RAY DIFFRACTIONr_scangle_it4.8552.454828
X-RAY DIFFRACTIONr_scangle_other4.8522.455829
X-RAY DIFFRACTIONr_lrange_it5.8417.1151230
X-RAY DIFFRACTIONr_lrange_other5.60816.5481195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.196930.1621532X-RAY DIFFRACTION99.267
1.693-1.7390.236750.1631491X-RAY DIFFRACTION99.7452
1.739-1.790.186750.1541482X-RAY DIFFRACTION99.7438
1.79-1.8450.201730.1621432X-RAY DIFFRACTION99.4055
1.845-1.9050.185740.1591369X-RAY DIFFRACTION99.5172
1.905-1.9720.199860.1611318X-RAY DIFFRACTION99.9288
1.972-2.0460.181640.1491293X-RAY DIFFRACTION99.7794
2.046-2.1290.184600.1421248X-RAY DIFFRACTION99.2413
2.129-2.2240.178660.1541174X-RAY DIFFRACTION99.5185
2.224-2.3320.192610.1481139X-RAY DIFFRACTION99.2556
2.332-2.4580.165580.1511093X-RAY DIFFRACTION99.3097
2.458-2.6070.223520.1711024X-RAY DIFFRACTION99.6296
2.607-2.7860.169550.175972X-RAY DIFFRACTION99.2271
2.786-3.0090.208500.178885X-RAY DIFFRACTION99.1516
3.009-3.2950.171410.164830X-RAY DIFFRACTION98.307
3.295-3.6810.163400.144750X-RAY DIFFRACTION98.75
3.681-4.2470.182360.137669X-RAY DIFFRACTION98.4637
4.247-5.1920.113400.14552X-RAY DIFFRACTION98.5025
5.192-7.3030.216320.18439X-RAY DIFFRACTION98.3299

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