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- PDB-8aol: Crystal structure of S-layer protein SlpX from Lactobacillus acid... -

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Basic information

Entry
Database: PDB / ID: 8aol
TitleCrystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain III (aa 363-499)
ComponentsSlpX
KeywordsCELL ADHESION / Surface Layer / SlpX / Cell wall binding
Function / homologySurface layer protein A domain / Surface layer protein A domain / metal ion binding / ACETATE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / SlpX
Function and homology information
Biological speciesLactobacillus acidophilus ATCC 4796 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSagmeister, T. / Damisch, E. / Eder, M. / Dordic, A. / 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
DepositionAug 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 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

Downloads & links

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Assembly

Deposited unit
A: SlpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,68310
Polymers17,0321
Non-polymers6509
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-109 kcal/mol
Surface area8310 Å2
Unit cell
Length a, b, c (Å)133.174, 133.174, 70.572
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-810-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SlpX


Mass: 17032.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus ATCC 4796 (bacteria)
Gene: slpX, LBA0512 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FLN0

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Non-polymers , 6 types, 152 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.3 Å3/Da / Density % sol: 76.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Wizard 1/2 screen condition 66 (20 % w/v PEG 3000, 200 mM Ca(OAc)2, 100 mM Tris base/HCl pH 7.0) with protein end ...Details: Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Wizard 1/2 screen condition 66 (20 % w/v PEG 3000, 200 mM Ca(OAc)2, 100 mM Tris base/HCl pH 7.0) with protein end concentration of 5 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: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→48.432 Å / Num. obs: 14935 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.065 / Rrim(I) all: 0.209 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.98-48.4315.80.0923490.9970.0310.097
2.4-2.4919.41.51615180.8440.4961.596

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ALU

8alu


Resolution: 2.4→48.432 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.17 / SU B: 6.849 / SU ML: 0.138 / Average fsc free: 0.8733 / Average fsc work: 0.8785 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.205 766 5.136 %
Rwork0.1779 14148 -
all0.179 --
obs-14914 99.966 %
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: 46.79 Å2
Baniso -1Baniso -2Baniso -3
1--3.069 Å2-1.534 Å2-0 Å2
2---3.069 Å20 Å2
3---9.955 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 29 143 1315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131225
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151086
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.6771641
X-RAY DIFFRACTIONr_angle_other_deg1.331.5932483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6585137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37520.95973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67715197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.794159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
X-RAY DIFFRACTIONr_nbd_refined0.1890.2215
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21001
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2549
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1670.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.224
X-RAY DIFFRACTIONr_nbd_other0.2120.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2120.23
X-RAY DIFFRACTIONr_mcbond_it3.7484.568554
X-RAY DIFFRACTIONr_mcbond_other3.6154.553548
X-RAY DIFFRACTIONr_mcangle_it5.1816.834685
X-RAY DIFFRACTIONr_mcangle_other5.216.84686
X-RAY DIFFRACTIONr_scbond_it11.1345.105671
X-RAY DIFFRACTIONr_scbond_other11.1255.106672
X-RAY DIFFRACTIONr_scangle_it13.8697.462956
X-RAY DIFFRACTIONr_scangle_other13.8627.463957
X-RAY DIFFRACTIONr_lrange_it16.47551.2621357
X-RAY DIFFRACTIONr_lrange_other16.46951.2831358
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
2.4-2.4620.287670.33110140.32810810.650.6091000.301
2.462-2.530.346500.3389880.33910380.6930.6491000.309
2.53-2.6030.349490.2989750.310240.7210.7571000.268
2.603-2.6830.319590.2769270.2789860.7640.81000.242
2.683-2.770.254450.2379180.2389630.8390.8561000.206
2.77-2.8670.229420.2138830.2149250.9280.9031000.182
2.867-2.9750.201450.2018660.2019110.9210.9281000.178
2.975-3.0960.246460.1748300.1778760.9170.9421000.159
3.096-3.2330.236360.1977980.1998340.9230.9351000.184
3.233-3.390.214440.1967640.1978080.9540.9451000.184
3.39-3.5730.175480.1717120.1717600.9690.9661000.164
3.573-3.7880.201390.1596950.1617340.970.9731000.153
3.788-4.0480.156360.1486550.1486910.9710.9731000.144
4.048-4.370.166420.136030.1326450.9740.981000.136
4.37-4.7830.126260.1175700.1175970.9790.98299.83250.126
4.783-5.3410.224250.1245270.1295520.9690.981000.135
5.341-6.1550.125240.1464650.1454890.9830.9741000.156
6.155-7.5080.196190.1484090.154280.9690.9771000.162
7.508-10.4920.176160.1563320.1573480.9680.9751000.183
10.492-48.4320.28180.1932170.1962250.9360.9711000.236

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