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- PDB-8q1o: S-layer protein SlpA from Lactobacillus amylovorus, domain I (aa ... -

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Basic information

Entry
Database: PDB / ID: 8q1o
TitleS-layer protein SlpA from Lactobacillus amylovorus, domain I (aa 32-209), important for Self-assembly
ComponentsS-layer
KeywordsSTRUCTURAL PROTEIN / Self assembly / S-layer
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: 3.401 Å
AuthorsSagmeister, T. / Grininger, C. / 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
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 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: S-layer
B: S-layer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9744
Polymers38,7842
Non-polymers1902
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-14 kcal/mol
Surface area22820 Å2
Unit cell
Length a, b, c (Å)133.194, 43.854, 86.384
Angle α, β, γ (deg.)90.000, 95.498, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 32 - 209 / Label seq-ID: 1 - 178

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein S-layer


Mass: 19392.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus amylovorus (bacteria) / Gene: LA2_00970 / Production host: Escherichia coli (E. coli) / References: UniProt: E4SK47
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Condition: 1.0 M Ammonium formate, 0.1 M Sodium acetate pH 5.0, 8 % w/v PGA with protein end concentration of 7.5 ...Details: Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Condition: 1.0 M Ammonium formate, 0.1 M Sodium acetate pH 5.0, 8 % w/v PGA with protein end concentration of 7.5 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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0047 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0047 Å / Relative weight: 1
ReflectionResolution: 3.4→42.993 Å / Num. obs: 7031 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.191 / Rrim(I) all: 0.278 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-42.9930.0544080.9970.0530.076
3.4-3.673.40.64314310.8540.6030.883

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.401→42.993 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.835 / SU B: 53.987 / SU ML: 0.767 / Cross valid method: FREE R-VALUE / ESU R Free: 0.731
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3306 334 4.774 %
Rwork0.2506 6662 -
all0.254 --
obs-6996 98.702 %
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: 74.477 Å2
Baniso -1Baniso -2Baniso -3
1--2.589 Å2-0 Å2-9.292 Å2
2--6.019 Å20 Å2
3----1.612 Å2
Refinement stepCycle: LAST / Resolution: 3.401→42.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 10 16 2702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0112730
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162530
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.6583738
X-RAY DIFFRACTIONr_angle_other_deg0.4241.5775810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8385354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.16456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24410424
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.32810118
X-RAY DIFFRACTIONr_chiral_restr0.0570.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02616
X-RAY DIFFRACTIONr_nbd_refined0.1980.2477
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22248
X-RAY DIFFRACTIONr_nbtor_refined0.170.21334
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21526
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3060.241
X-RAY DIFFRACTIONr_nbd_other0.2590.2179
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3460.24
X-RAY DIFFRACTIONr_mcbond_it5.6427.3531422
X-RAY DIFFRACTIONr_mcbond_other5.6287.3541422
X-RAY DIFFRACTIONr_mcangle_it9.36813.2041774
X-RAY DIFFRACTIONr_mcangle_other9.36913.2051775
X-RAY DIFFRACTIONr_scbond_it4.9647.7531308
X-RAY DIFFRACTIONr_scbond_other4.8567.7291301
X-RAY DIFFRACTIONr_scangle_it8.5914.0791964
X-RAY DIFFRACTIONr_scangle_other8.43314.031953
X-RAY DIFFRACTIONr_lrange_it13.06182.6422870
X-RAY DIFFRACTIONr_lrange_other13.05482.6622870
X-RAY DIFFRACTIONr_ncsr_local_group_10.2070.054431
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.206880.05006
12AX-RAY DIFFRACTIONLocal ncs0.206880.05006
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
3.401-3.4880.365280.3754780.3745160.9010.86498.0620.364
3.488-3.5830.385220.3694730.375000.830.869990.337
3.583-3.6860.651300.4964450.5074940.6770.86896.15380.487
3.686-3.7990.298240.3734170.3684650.9260.90394.83870.365
3.799-3.9230.353140.2784490.284640.9020.94299.78450.255
3.923-4.0590.293210.2624190.2654410.9670.95399.77320.243
4.059-4.2110.276220.2373930.2394170.9350.9699.52040.216
4.211-4.3810.263310.2084090.2124420.9420.96999.54750.193
4.381-4.5740.301190.1833610.1893820.9410.97699.47640.169
4.574-4.7940.372210.1843620.1933860.9380.97799.22280.174
4.794-5.050.196170.1883480.1883670.980.97799.4550.171
5.05-5.3520.239160.1633220.1673410.9610.98299.12020.15
5.352-5.7150.251120.1893050.1913200.9640.97799.06250.175
5.715-6.1640.252100.1893020.1913130.9660.97799.68050.177
6.164-6.7380.223120.1882640.1892770.970.97499.6390.17
6.738-7.5110.36880.2282550.2332640.8870.96699.62120.216
7.511-8.6290.29120.2152150.2192280.9520.96699.56140.21
8.629-10.4630.32390.2111920.2162040.9520.97498.52940.214
10.463-14.3770.43820.1941580.1961620.9250.98298.76540.198
14.377-42.9930.34240.337950.3381010.9560.92198.01980.367

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