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

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Basic information

Entry
Database: PDB / ID: 6hhu
TitleStructure of the Bacillus anthracis Sap S-layer assembly domain
Components
  • Nanobody AF694
  • S-layer protein sap
  • nanobody AF684
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 / SAD / Resolution: 2.7 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
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer protein sap
G: nanobody AF684
H: Nanobody AF694


Theoretical massNumber of molelcules
Total (without water)93,9693
Polymers93,9693
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy, protein forms 2D lattices on bacterial surface and planar and tubular lattices in vitro., SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-13 kcal/mol
Surface area43050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.553, 115.114, 152.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-918-

HOH

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Components

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


Mass: 64944.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 AF684


Mass: 14110.615 Da / Num. of mol.: 1
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 AF694


Mass: 14913.369 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG (2-Amino-2-(hydroxymethyl) propane-1,3-diol) buffer at pH 6.0, 25 % w/v polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.69→150 Å / Num. obs: 26723 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 72.18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.065 / Rrim(I) all: 0.23 / Net I/σ(I): 8.3
Reflection shellResolution: 2.69→2.73 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1282 / CC1/2: 0.658 / Rpim(I) all: 0.537 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia20.5.48data reduction
xia20.5.48data scaling
SHARP2.8phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→32.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 1.373 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.305 / SU Rfree Blow DPI: 0.325 / SU Rfree Cruickshank DPI: 0.332
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1304 4.95 %RANDOM
Rwork0.186 ---
obs0.19 26344 99.8 %-
Displacement parametersBiso mean: 65.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.7087 Å20 Å20 Å2
2--0.1676 Å20 Å2
3---0.5411 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.7→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6259 0 0 114 6373
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016338HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.388575HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2235SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1071HARMONIC5
X-RAY DIFFRACTIONt_it6338HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion23.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion861SEMIHARMONIC5
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_contact6702SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.81 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3568 142 4.91 %
Rwork0.2469 2750 -
all0.2524 2892 -
obs--98.44 %
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)
11.830.3491-1.43180.77280.31643.98720.16180.0771-0.1193-0.1191-0.03470.0765-0.03710.1669-0.127-0.0139-0.01160.061-0.12260.03750.0832152.94496.8707154.662
23.78051.159-2.4094.9206-3.16523.9317-0.0340.0247-0.06850.02660.0520.1467-0.1407-0.0951-0.018-0.2232-0.010.0194-0.1602-0.05230.1116132.67494.634176.151
33.3626-0.7058-0.37754.7264-1.59662.51040.1775-0.2190.70630.0739-0.0211-0.0002-0.0793-0.1333-0.1564-0.16670.05210.1458-0.2336-0.06560.1935154.51962.3985174.975
41.6730.69531.98591.76710.58587.1817-0.23450.1095-0.0957-0.13610.27460.262-0.3708-0.1648-0.0401-0.1920.021-0.0706-0.179800.1125176.20841.6472145.351
51.0040.16550.42031.3081-0.55298.90930.28230.4911-0.4883-0.24850.23760.15860.92090.4699-0.5199-0.15830.16220.0367-0.0274-0.1120.114183.00624.5225146.497
60.8287-1.36471.238300.4925.38610.09310.1487-0.5240.12-0.00490.44141.08851.0408-0.08830.19290.25590.0285-0.1815-0.13440.087185.22413.8692148.393
72.9668-2.4947-0.4332.59171.1181.75930.1905-0.06590.4879-0.02090.131-0.21590.0942-0.064-0.3216-0.2079-0.08290.028-0.21240.02340162.22730.2754177.28
86.7387-3.7576-0.02573.269-0.87562.34910.2408-0.23650.1231-0.2205-0.1978-0.24280.0170.1955-0.043-0.1033-0.04840.0332-0.14150.02580.238157.9637.1058179.963
93.76360.17351.95491.3787-0.13263.2457-0.19080.06350.0538-0.0634-0.0533-0.20640.18840.34420.2442-0.1236-0.00610.057-0.17910.01930.1385160.81597.465178.939
100.8972-0.8896-0.38834.380.28072.19340.08980.29690.23920.1534-0.14430.1243-0.1114-0.13050.0545-0.0880.07430.0012-0.09580.09750.0279155.721108.017131.728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|216 - A|290 }
2X-RAY DIFFRACTION2{ A|291 - A|386 }
3X-RAY DIFFRACTION3{ A|387 - A|490 }
4X-RAY DIFFRACTION4{ A|491 - A|592 }
5X-RAY DIFFRACTION5{ A|593 - A|631 }
6X-RAY DIFFRACTION6{ A|632 - A|696 }
7X-RAY DIFFRACTION7{ A|697 - A|764 }
8X-RAY DIFFRACTION8{ A|765 - A|811 }
9X-RAY DIFFRACTION9{ G|1 - G|119 }
10X-RAY DIFFRACTION10{ H|1 - H|123 }

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