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- PDB-8bex: Structure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal pr... -

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Basic information

Entry
Database: PDB / ID: 8bex
TitleStructure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein at pH 3
ComponentsCry49Aa protein
KeywordsTOXIN / Lysinibacillus sphaericus / Bacillus thuringiensis / Tpp49Aa1 / Cry48Aa1 / XFEL / SFX / mosquitoes / culex quinquefasciatus
Function / homologyRicin B-like lectins / toxin activity / Cry49Aa protein
Function and homology information
Biological speciesLysinibacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsWilliamson, L.J. / Rizkallah, P.J. / Berry, C. / Oberthur, D. / Galchenkova, M. / Yefanov, O. / Bean, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002774/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein elucidated from natural crystals using MHz-SFX.
Authors: Williamson, L.J. / Galchenkova, M. / Best, H.L. / Bean, R.J. / Munke, A. / Awel, S. / Pena, G. / Knoska, J. / Schubert, R. / Dorner, K. / Park, H.W. / Bideshi, D.K. / Henkel, A. / Kremling, ...Authors: Williamson, L.J. / Galchenkova, M. / Best, H.L. / Bean, R.J. / Munke, A. / Awel, S. / Pena, G. / Knoska, J. / Schubert, R. / Dorner, K. / Park, H.W. / Bideshi, D.K. / Henkel, A. / Kremling, V. / Klopprogge, B. / Lloyd-Evans, E. / Young, M.T. / Valerio, J. / Kloos, M. / Sikorski, M. / Mills, G. / Bielecki, J. / Kirkwood, H. / Kim, C. / de Wijn, R. / Lorenzen, K. / Xavier, P.L. / Rahmani Mashhour, A. / Gelisio, L. / Yefanov, O. / Mancuso, A.P. / Federici, B.A. / Chapman, H.N. / Crickmore, N. / Rizkallah, P.J. / Berry, C. / Oberthur, D.
History
DepositionOct 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cry49Aa protein
B: Cry49Aa protein


Theoretical massNumber of molelcules
Total (without water)95,6232
Polymers95,6232
Non-polymers00
Water6,612367
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-5 kcal/mol
Surface area34560 Å2
Unit cell
Length a, b, c (Å)79.890, 82.840, 157.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 49 - 464 / Label seq-ID: 1 - 416

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cry49Aa protein / Crystal toxin


Mass: 47811.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysinibacillus sphaericus (bacteria) / Gene: Cry49Aa1, cry49Aa / Production host: Bacillus thuringiensis (bacteria) / References: UniProt: A7WK53
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 298 K / Method: in cell / pH: 3 / Details: Naturally grown

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.33 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 1.78→36.01 Å / Num. obs: 100541 / % possible obs: 99.51 % / Redundancy: 183.7 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 10.5
Reflection shellResolution: 1.78→1.8 Å / Num. unique obs: 6177 / CC1/2: 0.138 / % possible all: 92.76
Serial crystallography sample deliveryMethod: injection

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.27 Å35.98 Å
Translation7.27 Å35.98 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELAmbigatordata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WA1, 5FOY, 5G37

3wa1

5foy

5g37


Resolution: 1.78→36.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.896 / SU ML: 0.105 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 5033 5 %RANDOM
Rwork0.1887 ---
obs0.1899 95333 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.26 Å2 / Biso mean: 32.724 Å2 / Biso min: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0 Å2
2--0.1 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.78→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6748 0 0 367 7115
Biso mean---39.39 -
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137046
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176516
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.6489611
X-RAY DIFFRACTIONr_angle_other_deg1.2851.5814914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5665866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63222.057457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.964151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1051564
X-RAY DIFFRACTIONr_chiral_restr0.0690.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021840
Refine LS restraints NCS

Ens-ID: 1 / Number: 13818 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 386 -
Rwork0.44 6431 -
all-6817 -
obs--92.05 %
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)
13.1764-0.6010.09643.03821.26593.65450.14240.5279-0.5196-0.2271-0.27190.3430.1696-0.15520.12960.11840.0524-0.05310.2559-0.13360.1141-12.2708-24.5639-42.3154
20.65160.30350.47711.5131.60063.21010.0052-0.08590.05720.0056-0.0448-0.0549-0.21140.23830.03950.0893-0.0319-0.0080.15120.02280.0166-3.73081.4857-7.0371
32.8964-0.53-1.16792.6825-0.61074.4856-0.1673-0.3432-0.33880.43140.23570.42890.0191-0.3433-0.06840.220.08590.1030.26690.11970.1077-4.6167-32.31542.9058
41.87040.3099-1.54870.5888-0.41853.1105-0.04040.0290.0807-0.05160.0377-0.0397-0.22610.19350.00270.107-0.0245-0.01910.11250.0060.013621.4709-24.731-32.5325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 214
2X-RAY DIFFRACTION2A215 - 463
3X-RAY DIFFRACTION3B49 - 214
4X-RAY DIFFRACTION4B215 - 463

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