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- PDB-8opr: Structure of the EA1 surface layer of Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 8opr
TitleStructure of the EA1 surface layer of Bacillus anthracis
Components
  • Nanobody 632
  • Nanobody 643
  • S-layer protein EA1
KeywordsSTRUCTURAL PROTEIN / S-layer / EA1 / anthrax
Function / homologyexternal encapsulating structure organization / S-layer / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / structural molecule activity / extracellular region / ACETATE ION / S-layer protein EA1
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.811 Å
AuthorsSogues, A. / Remaut, H.
Funding support Belgium, European Union, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G065220N Belgium
Research Foundation - Flanders (FWO)1253121N Belgium
European Molecular Biology Organization (EMBO)ALTF-709-2021European Union
CitationJournal: Nat Commun / Year: 2023
Title: Structure and function of the EA1 surface layer of Bacillus anthracis.
Authors: Sogues, A. / Fioravanti, A. / Jonckheere, W. / Pardon, E. / Steyaert, J. / Remaut, H.
History
DepositionApr 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 EA1
B: Nanobody 643
C: Nanobody 632
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,46015
Polymers99,6603
Non-polymers80012
Water15,493860
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-81 kcal/mol
Surface area43200 Å2
Unit cell
Length a, b, c (Å)72.927, 74.297, 87.649
Angle α, β, γ (deg.)107.85, 101.14, 112.42
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein S-layer protein EA1


Mass: 70793.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: eag, BA_0887, GBAA_0887, BAS0842 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P94217

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Antibody , 2 types, 2 molecules BC

#2: Antibody Nanobody 643


Mass: 13861.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Antibody Nanobody 632


Mass: 15005.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 872 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulfate and 0.1 M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98112 Å / Relative weight: 1
ReflectionResolution: 1.811→62.35 Å / Num. obs: 73143 / % possible obs: 99 % / Redundancy: 3.1 % / CC1/2: 0.997 / Net I/σ(I): 9.1
Reflection shellResolution: 1.811→2.038 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 3659 / CC1/2: 0.689

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.811→63.37 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 3807 -RANDOM
Rwork0.2036 ---
obs0.2056 73143 53 %-
Displacement parametersBiso mean: 55.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.2233 Å24.872 Å23.7147 Å2
2--1.517 Å23.3301 Å2
3----3.7403 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.811→63.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6670 0 43 860 7573
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086810HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.039256HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2320SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1174HARMONIC5
X-RAY DIFFRACTIONt_it6795HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion919SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5724SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion18.05
LS refinement shellResolution: 1.811→1.96 Å
RfactorNum. reflection% reflection
Rfree0.2752 86 -
Rwork0.2699 --
obs--5.01 %
Refinement TLS params.

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)
10.0782-0.078-0.022-0.0043-0.02180.0787-0.02970.03490.06660.0349-0.03020.04190.06660.04190.060.01750.09840.0720.00790.0674-0.0896-45.996620.14716.4806
26.4858-2.16741.034.4902-3.09146.8957-0.24480.5715-1.36790.5715-0.3429-0.0449-1.3679-0.04490.5877-0.00720.0521-0.188-0.06950.14040.1628-37.756357.925211.6619
312.8833-2.2382-6.80573.40340.96947.4585-0.2256-0.23380.3548-0.23380.01830.69920.35480.69920.2072-0.22180.32740.15840.2868-0.24250.286-11.797623.8636-26.0346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A212 - 862
2X-RAY DIFFRACTION1{ A|* }A901 - 905
3X-RAY DIFFRACTION2{ B|* }B1 - 120
4X-RAY DIFFRACTION3{ C|* }C1 - 125

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