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- PDB-6qx4: Structure of the Bacillus anthracis Sap S-layer assembly domain -

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Basic information

Entry
Database: PDB / ID: 6qx4
TitleStructure of the Bacillus anthracis Sap S-layer assembly domain
Components
  • Nanobody NbAF683
  • Nanobody NbAF694
  • S-layer protein sap
KeywordsSTRUCTURAL PROTEIN / S-layer / exoskeleton / bacterial cell surface
Function / homology
Function and homology information


S-layer / extracellular region
Similarity search - Function
SbsA, Ig-like domain / Bacterial Ig-like domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsRemaut, H. / Fioravanti, A.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - FlandersG028113N Belgium
CitationJournal: Nat Microbiol / Year: 2019
Title: Structure of S-layer protein Sap reveals a mechanism for therapeutic intervention in anthrax.
Authors: Fioravanti, A. / Van Hauwermeiren, F. / Van der Verren, S.E. / Jonckheere, W. / Goncalves, A. / Pardon, E. / Steyaert, J. / De Greve, H. / Lamkanfi, M. / Remaut, H.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer protein sap
B: S-layer protein sap
C: Nanobody NbAF683
D: Nanobody NbAF694
E: Nanobody NbAF683
H: Nanobody NbAF694


Theoretical massNumber of molelcules
Total (without water)187,6716
Polymers187,6716
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy, TEM confirms 2D lattice formation of the isolated Sap assembly domain, SAXS, SAXS confirms monomeric state of deposited complex, light scattering, ...Evidence: scanning transmission electron microscopy, TEM confirms 2D lattice formation of the isolated Sap assembly domain, SAXS, SAXS confirms monomeric state of deposited complex, light scattering, DLS show high MW polymer formation of the isolated Sap protein (chain A, B), and stabilization as monomeric unit when in complex with nanobodies NbAF694 and Nb683
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-20 kcal/mol
Surface area80680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.230, 79.910, 81.230
Angle α, β, γ (deg.)88.660, 82.000, 85.590
Int Tables number1
Space group name H-MP1

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Components

#1: Protein S-layer protein sap / / Surface array protein / Surface layer protein


Mass: 64771.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein fragment corresponding to the S-layer assembly domain of the B. anthracis surface array protein Sap
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sap, BA_0885, GBAA_0885, BAS0841 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P49051
#2: Antibody Nanobody NbAF683


Mass: 14150.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Antibody Nanobody NbAF694


Mass: 14913.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M SPG (2-Amino-2-(hydroxymethyl) propane-1,3-diol) buffer at pH 6.0, and 25 % w/v polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 3.27→80.44 Å / Num. obs: 26634 / % possible obs: 97.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 72.64 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.079 / Net I/σ(I): 4.4
Reflection shellResolution: 3.27→3.37 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.518 / Num. unique obs: 2339 / CC1/2: 0.74 / Rpim(I) all: 0.392 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSJan 26, 2018 (BUILT 20180808)data reduction
autoPROC1.0.5data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HHU

6hhu


Resolution: 3.27→35 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.474
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1312 4.93 %RANDOM
Rwork0.173 ---
obs0.175 26634 93.6 %-
Displacement parametersBiso max: 198.37 Å2 / Biso mean: 76.73 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1--6.105 Å2-1.9073 Å21.5985 Å2
2--3.0026 Å2-0.7963 Å2
3---3.1024 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 3.27→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12539 0 0 28 12567
Biso mean---31.9 -
Num. residues----1662
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4467SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2147HARMONIC5
X-RAY DIFFRACTIONt_it12707HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1726SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13578SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12707HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17201HARMONIC21.33
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion21.86
LS refinement shellResolution: 3.27→3.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2671 122 4.95 %
Rwork0.212 2343 -
all0.2147 2465 -
obs--76.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.4177-1.3032-0.34054.47390.84362.7258-0.2193-0.42740.0265-0.26320.2168-0.0246-0.12520.15850.0026-0.34660.00740.0149-0.1025-0.0340.020137.4387-0.534159.6477
25.9553-0.31782.63174.17971.9567.56460.09280.1940.9232-0.5497-0.2984-0.0773-0.9226-0.37720.2057-0.25570.0208-0.0146-0.19970.1037-0.060613.202511.989445.9915
33.1184-0.06421.112310.30651.68331.93650.17480.22720.16771.1859-0.3347-0.1670.48390.19740.15980.010.08210.1771-0.1741-0.1016-0.120113.4065-26.503840.2947
43.4587-1.180.16221.24780.50792.38280.10730.5044-0.1235-0.3853-0.178-0.1837-0.4460.18650.0707-0.0867-0.01840.1988-0.30140.0835-0.132837.1787-68.498833.7463
51.86080.55240.860110.11894.20132.97160.03070.18440.03790.4862-0.02060.46480.0551-0.3677-0.0102-0.11940.06340.1420.0690.0183-0.19394.2826-47.730824.228
67.06610.3346-0.362.87160.274.2404-0.0472-0.4137-0.180.1048-0.33030.2885-0.4222-0.2590.3775-0.2198-0.03170.0595-0.0289-0.0306-0.15531.5828-56.75123.758
75.89622.88385.0238.19714.00545.7672-0.2360.05450.3442-0.3592-0.2927-0.3552-1.32440.29550.52870.3488-0.3518-0.11-0.17720.226-0.393652.2133-40.1308-10.8634
82.36620.47242.20274.7560.80974.6049-0.1870.14620.1958-0.75390.26270.2880.398-0.193-0.0758-0.1273-0.1857-0.0672-0.1802-0.0364-0.191854.0502-35.393827.5854
93.995-0.2604-1.25883.46690.89872.5032-0.0752-0.03380.12190.3306-0.06270.6871-0.1146-0.49450.1379-0.12180.07970.1883-0.22160.0463-0.259634.7348-29.843172.8337
101.45221.50860.18353.6835.3027.06640.2636-0.21220.06870.10140.1459-0.44150.27620.1937-0.4095-0.22890.0122-0.0797-0.2180.0229-0.027164.8443-18.931547.625
11-0.2672-1.09710.05521.03490.2795.1985-0.2539-1.1767-0.4090.5936-0.12880.36160.36180.110.3827-0.16420.11820.2420.3576-0.0019-0.001115.0584-2.693275.5753
126.81820.5076-0.28411.50960.06335.8611-0.1583-1.0905-0.97020.2316-0.15350.43920.89760.06410.3118-0.3758-0.06390.1544-0.0540.19410.001112.1684-8.60167.554
136.3106-4.1254-0.595110.7263-4.25144.1641-0.3863-0.8785-0.65750.53990.27810.21580.49280.47110.1082-0.2879-0.05040.0617-0.00510.1466-0.109719.8223-5.765167.3776
149.6051-0.392-0.02243.2253-0.56795.77290.0871-0.54440.49050.0325-0.1215-0.3267-0.22380.07270.0345-0.303-0.05520.0763-0.1158-0.18070.010362.70583.392966.2917
158.2848-1.20710.1577.31973.61522.65890.1019-0.96420.84550.22030.0942-0.31850.04540.2294-0.1961-0.37450.0303-0.00580.095-0.1789-0.061263.19115.984572.3838
164.65821.10380.05064.82712.6181-0.17830.04610.0599-0.1509-0.00750.0948-0.1383-0.0945-0.0543-0.1409-0.3343-0.05550.1344-0.0524-0.0763-0.05360.5059-1.071561.4779
17-0.2467-2.54330.48692.6776-1.74740.6173-0.1955-0.0983-0.7901-0.03720.0503-0.08330.28210.16790.1452-0.0843-0.0211-0.0015-0.03450.07630.244856.7298-69.12983.6715
186.3996-2.02552.39431.38930.38555.0548-0.1849-0.4825-0.41020.12180.0986-0.0763-0.09250.87670.0863-0.1893-0.08440.03220.01190.1466-0.194258.342-60.60559.3691
194.045-0.19270.00220.4657-2.29598.60770.0178-0.4873-0.08130.22850.1810.2205-0.08010.2546-0.1989-0.1654-0.1212-0.0077-0.05820.1068-0.101350.6859-61.9777.0745
2010.26110.1369-4.9665.62732.82887.4091-0.14931.1376-0.836-0.467-0.04420.15880.5365-0.76670.1934-0.35740.01910.04290.0576-0.3974-0.18877.0779-66.00961.7926
219.83212.0225-3.727410.3174.07655.0802-0.12731.0537-0.98460.30220.01490.06230.8612-0.410.1124-0.2077-0.14050.21040.308-0.3157-0.18117.0914-72.0954-0.871
227.3610.1045-4.402-0.02231.176311.5531-0.06770.3169-0.16030.10480.03350.1719-0.0319-0.45460.0342-0.47910.16810.0086-0.1463-0.2219-0.27058.963-61.07136.2199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|216 - A|298 }A216 - 298
2X-RAY DIFFRACTION2{ A|299 - A|386 }A299 - 386
3X-RAY DIFFRACTION3{ A|387 - A|492 }A387 - 492
4X-RAY DIFFRACTION4{ A|493 - A|708 }A493 - 708
5X-RAY DIFFRACTION5{ A|709 - A|808 }A709 - 808
6X-RAY DIFFRACTION6{ B|216 - B|298 }B216 - 298
7X-RAY DIFFRACTION7{ B|299 - B|386 }B299 - 386
8X-RAY DIFFRACTION8{ B|387 - B|492 }B387 - 492
9X-RAY DIFFRACTION9{ B|493 - B|708 }B493 - 708
10X-RAY DIFFRACTION10{ B|709 - B|808 }B709 - 808
11X-RAY DIFFRACTION11{ C|1 - C|27 }C1 - 27
12X-RAY DIFFRACTION12{ C|28 - C|87 }C28 - 87
13X-RAY DIFFRACTION13{ C|88 - C|119 }C88 - 119
14X-RAY DIFFRACTION14{ D|1 - D|63 }D1 - 63
15X-RAY DIFFRACTION15{ D|64 - D|90 }D64 - 90
16X-RAY DIFFRACTION16{ D|91 - D|123 }D91 - 123
17X-RAY DIFFRACTION17{ E|1 - E|27 }E1 - 27
18X-RAY DIFFRACTION18{ E|28 - E|87 }E28 - 87
19X-RAY DIFFRACTION19{ E|88 - E|119 }E88 - 119
20X-RAY DIFFRACTION20{ H|1 - H|63 }H1 - 63
21X-RAY DIFFRACTION21{ H|64 - H|90 }H64 - 90
22X-RAY DIFFRACTION22{ H|91 - H|123 }H91 - 123

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