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

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Basic information

Entry
Database: PDB / ID: 7qle
TitleCrystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I (aa 32-198)
ComponentsS-layer protein
KeywordsSTRUCTURAL PROTEIN / Surface Layer Protein / SlpA / S-layer / self-assembly / Lactobacillus acidophilus
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
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSagmeister, T. / Eder, M. / Vejzovic, D. / Dordic, A. / 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Jun 26, 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 protein
B: S-layer protein


Theoretical massNumber of molelcules
Total (without water)38,9642
Polymers38,9642
Non-polymers00
Water2,324129
1
A: S-layer protein


Theoretical massNumber of molelcules
Total (without water)19,4821
Polymers19,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-layer protein


Theoretical massNumber of molelcules
Total (without water)19,4821
Polymers19,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.127, 39.036, 60.058
Angle α, β, γ (deg.)90.000, 101.662, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 32 - 193 / Label seq-ID: 23 - 184

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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

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Components

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


Mass: 19482.000 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.61 %
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; JCSG+ screen condition A5 (0.2 M Magnesium formate dihydrate, 20 % w/v PEG 3350) 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; JCSG+ screen condition A5 (0.2 M Magnesium formate dihydrate, 20 % w/v PEG 3350) 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: ESRF / Beamline: ID23-1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.6→48.37 Å / Num. obs: 9254 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.137 / Rrim(I) all: 0.198 / Net I/σ(I): 7.1
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.574 / Num. unique obs: 893 / CC1/2: 0.666 / Rpim(I) all: 0.547 / Rrim(I) all: 0.794

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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: 7QLD

7qld


Resolution: 2.6→48.367 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.966 / SU ML: 0.297 / Cross valid method: FREE R-VALUE / ESU R Free: 0.352
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2583 462 4.994 %
Rwork0.2003 8790 -
all0.203 --
obs-9252 99.111 %
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: 32.184 Å2
Baniso -1Baniso -2Baniso -3
1-2.068 Å2-0 Å2-0.156 Å2
2--1.597 Å2-0 Å2
3----3.318 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 0 129 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132209
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152076
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6433022
X-RAY DIFFRACTIONr_angle_other_deg1.2711.5784763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2375305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64827.94978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08915323
X-RAY DIFFRACTIONr_chiral_restr0.0580.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_nbd_refined0.2070.2335
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21782
X-RAY DIFFRACTIONr_nbtor_refined0.1510.21117
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21172
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.268
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1050.214
X-RAY DIFFRACTIONr_nbd_other0.1760.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.27
X-RAY DIFFRACTIONr_mcbond_it2.9063.391238
X-RAY DIFFRACTIONr_mcbond_other2.9023.3891237
X-RAY DIFFRACTIONr_mcangle_it4.8365.0391537
X-RAY DIFFRACTIONr_mcangle_other4.8345.0411538
X-RAY DIFFRACTIONr_scbond_it2.7083.566971
X-RAY DIFFRACTIONr_scbond_other2.7063.568972
X-RAY DIFFRACTIONr_scangle_it4.4975.2581485
X-RAY DIFFRACTIONr_scangle_other4.4965.2591486
X-RAY DIFFRACTIONr_lrange_it8.22440.2932197
X-RAY DIFFRACTIONr_lrange_other8.22340.3232196
X-RAY DIFFRACTIONr_ncsr_local_group_10.1050.053857
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.105480.05008
12BX-RAY DIFFRACTIONLocal ncs0.105480.05008
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
2.6-2.6680.388380.3136100.3176540.6950.75799.08260.289
2.668-2.7410.339310.3146490.3156890.760.77998.69380.286
2.741-2.820.357320.295990.2936350.7660.80399.37010.26
2.82-2.9060.39370.2555710.2646140.8110.83299.02280.229
2.906-3.0010.27210.2316120.2326370.850.86399.37210.206
3.001-3.1060.375280.2065360.2135700.8190.89798.94740.183
3.106-3.2230.254310.1895390.1935740.9250.92499.30310.167
3.223-3.3540.164250.1985180.1965470.9590.93899.26870.179
3.354-3.5020.226300.1994920.25240.9140.93899.61830.184
3.502-3.6720.241280.2054660.2074990.930.92298.9980.184
3.672-3.8690.386170.2134580.2194800.8620.91298.95830.198
3.869-4.1030.279220.1934380.1964630.9030.93599.35210.169
4.103-4.3840.216190.1444140.1474360.9380.96299.31190.139
4.384-4.7320.198190.1323730.1353970.9640.9798.74060.129
4.732-5.1780.186230.1493430.1523680.9660.96899.45650.141
5.178-5.7810.245200.1653250.173480.9540.95599.13790.149
5.781-6.660.159110.1782920.1773040.9770.95899.67110.166
6.66-8.1180.296150.152400.1592580.9380.96498.83720.142
8.118-11.3220.122100.1451960.1442090.9870.97698.56460.156
11.322-48.3670.34150.2741190.2761270.8540.94797.63780.298

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