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

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Basic information

Entry
Database: PDB / ID: 8bey
TitleStructure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein at pH 7
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: 1.62 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

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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
Water8,647480
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-4 kcal/mol
Surface area34380 Å2
Unit cell
Length a, b, c (Å)79.650, 83.110, 156.910
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.: 480 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 298 K / Method: in cell / pH: 7 / Details: Natural

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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: 1.62→24.98 Å / Num. obs: 132750 / % possible obs: 100 % / Redundancy: 1028.3 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 10.61
Reflection shellResolution: 1.62→1.64 Å / Num. unique obs: 8756 / CC1/2: 0.133
Serial crystallography sample deliveryMethod: injection

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.27 Å24.97 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: 1.62→24.98 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 5.008 / SU ML: 0.076 / SU R Cruickshank DPI: 0.0802 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 6673 5 %RANDOM
Rwork0.1762 ---
obs0.1771 125990 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.25 Å2 / Biso mean: 31.465 Å2 / Biso min: 16.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.62→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6748 0 0 480 7228
Biso mean---40.32 -
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137059
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176525
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.6489632
X-RAY DIFFRACTIONr_angle_other_deg1.3541.5814939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3715870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82422.052458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.112151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0281564
X-RAY DIFFRACTIONr_chiral_restr0.0680.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021843
Refine LS restraints NCS

Ens-ID: 1 / Number: 13894 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 472 -
Rwork0.374 9263 -
all-9735 -
obs--100 %
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)
12.3347-0.676-0.08512.69361.22663.6880.11410.5443-0.5039-0.2311-0.28680.34290.0992-0.27020.17280.0820.0545-0.05480.2499-0.16180.1367-12.1492-24.3164-42.2476
20.62050.08010.14941.33451.28742.77680.0236-0.06840.06150.0003-0.0307-0.0977-0.20660.19570.0070.0688-0.0349-0.01140.09040.01420.0208-3.74391.7558-6.9038
32.6932-0.2106-1.2832.3238-0.85843.7407-0.1173-0.2215-0.270.56330.12240.3549-0.1619-0.1851-0.00510.25180.06080.11770.12880.05950.0847-4.749-32.19782.9713
41.51950.3253-1.30820.7266-0.36712.6473-0.02280.03290.0624-0.03330.0124-0.0763-0.15320.16520.01030.0545-0.0176-0.00790.08460.01210.017821.6375-24.8067-32.3784
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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