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- PDB-7qfj: Crystal structure of S-layer protein SlpX from Lactobacillus acid... -

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Basic information

Entry
Database: PDB / ID: 7qfj
TitleCrystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain II (aa 194-362)
ComponentsSlpX
KeywordsSTRUCTURAL PROTEIN / SlpX / Self-assembly / Surface Layer Protein / S-layer / Lactobacillus acidophilus
Function / homologySurface layer protein A domain / Surface layer protein A domain / metal ion binding / SlpX
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSagmeister, T. / Pavkov-Keller, T. / Buhlheller, C. / Baek, M. / Read, R. / Baker, D.
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 1.1May 1, 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: SlpX
B: SlpX
C: SlpX
D: SlpX
E: SlpX
F: SlpX


Theoretical massNumber of molelcules
Total (without water)121,7876
Polymers121,7876
Non-polymers00
Water3,891216
1
A: SlpX


Theoretical massNumber of molelcules
Total (without water)20,2981
Polymers20,2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SlpX


Theoretical massNumber of molelcules
Total (without water)20,2981
Polymers20,2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SlpX


Theoretical massNumber of molelcules
Total (without water)20,2981
Polymers20,2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SlpX


Theoretical massNumber of molelcules
Total (without water)20,2981
Polymers20,2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: SlpX


Theoretical massNumber of molelcules
Total (without water)20,2981
Polymers20,2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: SlpX


Theoretical massNumber of molelcules
Total (without water)20,2981
Polymers20,2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.679, 143.016, 73.441
Angle α, β, γ (deg.)90.000, 96.699, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_3ens_1
d_4ens_1
d_5ens_1
d_6ens_1

NCS oper:
IDCodeMatrixVector
1given(0.999437603572, -0.0334894656605, -0.00171238337469), (-0.0275697202931, -0.849696232331, 0.526551254187), (-0.0190889258474, -0.526207913712, -0.850141661405)7.01893194781, -52.1809550163, 37.7509474327
2given(0.999884202476, -0.0122621906637, 0.00901223163781), (0.0070727726483, -0.14990879693, -0.988674531122), (0.0134743284075, 0.988623786525, -0.149804710176)16.3121452814, 32.7150488076, 32.6039244698
3given(-0.993792337929, -0.104790081824, 0.0373607792273), (-0.0788867227863, 0.90055747178, 0.427519736373), (-0.0784453570407, 0.421918568887, -0.903233661456)-19.8314714823, -20.9155321943, 71.9384297309
4given(-0.996183049888, -0.0445065633416, 0.0750899256565), (-0.0428505720502, -0.50011186711, -0.86489996465), (0.076047087982, -0.864816330902, 0.496295833364)-10.3385472346, 4.91208327697, -12.7394332798
5given(-0.999630482622, 0.0268322983713, -0.00435039960731), (-0.0155989602533, -0.435182045739, 0.900207342508), (0.0222614162093, 0.899942561962, 0.435439794366)1.30833192482, -38.7270316809, 11.706766177

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Components

#1: Protein
SlpX


Mass: 20297.803 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: slpX, LBA0512 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FLN0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Midas screen condition 50 (0.1M Tris, 50% v/v Pentaerythritol propoxylate (5/4 PO/OH)) with protein end concentration ...Details: Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Midas screen condition 50 (0.1M Tris, 50% v/v Pentaerythritol propoxylate (5/4 PO/OH)) with protein end concentration of 5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop, co-crystallization with 0.1 ul 2mM HgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9429 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9429 Å / Relative weight: 1
ReflectionResolution: 2.5→48.63 Å / Num. obs: 46501 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.053 / Rrim(I) all: 0.1 / Net I/σ(I): 17.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.6 / Num. unique obs: 4625 / CC1/2: 0.866 / Rpim(I) all: 0.384 / Rrim(I) all: 0.715

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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: RoseTTAfold ab initio prediction

Resolution: 2.5→46.028 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.178 / Average fsc free: 0.8808 / Average fsc work: 0.8994 / Cross valid method: FREE R-VALUE / ESU R: 0.424 / ESU R Free: 0.262
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2290 4.928 %RANDOM
Rwork0.2056 44181 --
all0.207 ---
obs-46471 99.927 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 47.942 Å2
Baniso -1Baniso -2Baniso -3
1--4.037 Å20 Å20.827 Å2
2--3.417 Å20 Å2
3---0.415 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7788 0 0 216 8004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0117904
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.64210768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4851026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17126.816358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.395151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.204156
X-RAY DIFFRACTIONr_chiral_restr0.0890.21155
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025968
X-RAY DIFFRACTIONr_nbd_refined0.2060.22793
X-RAY DIFFRACTIONr_nbtor_refined0.2880.25553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2302
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3170.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.216
X-RAY DIFFRACTIONr_mcbond_it4.3364.6884134
X-RAY DIFFRACTIONr_mcangle_it6.5787.0085150
X-RAY DIFFRACTIONr_scbond_it5.0634.8573770
X-RAY DIFFRACTIONr_scangle_it7.3547.1335618
X-RAY DIFFRACTIONr_lrange_it9.70661.0111093
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
2.5-2.5650.3761790.3232170.32333970.7210.77399.97060.287
2.565-2.6350.341560.30532030.30633590.8130.8211000.272
2.635-2.7110.3551690.2830570.28432270.7980.83499.9690.246
2.711-2.7940.31560.27329860.27431420.8510.8581000.239
2.794-2.8850.3371450.25129080.25530540.830.87999.96730.217
2.885-2.9860.2621450.23628330.23729790.9040.9199.96640.203
2.986-3.0980.2531360.21927070.2228430.8970.9141000.191
3.098-3.2240.31500.23625900.2427400.8590.891000.209
3.224-3.3670.2921160.22725120.23126300.8950.90899.9240.206
3.367-3.530.2321070.21124100.21225170.9260.9341000.193
3.53-3.720.2271360.19322650.19524010.9310.9461000.18
3.72-3.9440.2281100.19821720.19922830.9330.94399.95620.183
3.944-4.2140.2321070.18520230.18721300.940.9471000.173
4.214-4.5490.1911100.16218820.16319920.9540.9591000.15
4.549-4.9780.185800.15417630.15618430.9590.9641000.144
4.978-5.5580.193760.15315940.15516710.9620.96599.94020.143
5.558-6.4020.186760.17413880.17514650.9630.96599.93170.161
6.402-7.8030.205550.16111980.16312540.9510.96599.92030.151
7.803-10.880.17480.1589410.1589910.9730.97299.79820.155
10.88-46.0280.165330.1925320.195780.9660.95597.75090.198

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