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- PDB-6t19: Structure of mosquitocidal Cyt1A protoxin obtained by Serial Femt... -

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Basic information

Entry
Database: PDB / ID: 6t19
TitleStructure of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals soaked with DTT at pH 7
ComponentsType-1Aa cytolytic delta-endotoxin
KeywordsTOXIN / Mosquitocidal toxin / in vivo grown nanocrystals
Function / homologyDelta-endotoxin CytB / Delta-endotoxin CytB-like superfamily / Bacillus thuringiensis toxin / sporulation resulting in formation of a cellular spore / toxin activity / extracellular region / Type-1Aa cytolytic delta-endotoxin
Function and homology information
Biological speciesBacillus thuringiensis subsp. israelensis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTetreau, G. / Banneville, A.S. / Andreeva, E. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Young, I.D. / Boutet, S. / Coquelle, N. / Cascio, D. ...Tetreau, G. / Banneville, A.S. / Andreeva, E. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Young, I.D. / Boutet, S. / Coquelle, N. / Cascio, D. / Sawaya, M.R. / Sauter, N.K. / Colletier, J.P.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0018-01 France
French National Research AgencyANR-2018-CE11-0005-02 France
CitationJournal: Nat Commun / Year: 2020
Title: Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade.
Authors: Tetreau, G. / Banneville, A.S. / Andreeva, E.A. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Teulon, J.M. / Young, I.D. / Burke, N. / Grunewald, T.A. / Beaudouin, J. / Snigireva, I. / ...Authors: Tetreau, G. / Banneville, A.S. / Andreeva, E.A. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Teulon, J.M. / Young, I.D. / Burke, N. / Grunewald, T.A. / Beaudouin, J. / Snigireva, I. / Fernandez-Luna, M.T. / Burt, A. / Park, H.W. / Signor, L. / Bafna, J.A. / Sadir, R. / Fenel, D. / Boeri-Erba, E. / Bacia, M. / Zala, N. / Laporte, F. / Despres, L. / Weik, M. / Boutet, S. / Rosenthal, M. / Coquelle, N. / Burghammer, M. / Cascio, D. / Sawaya, M.R. / Winterhalter, M. / Gratton, E. / Gutsche, I. / Federici, B. / Pellequer, J.L. / Sauter, N.K. / Colletier, J.P.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: 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
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3782
Polymers27,3551
Non-polymers231
Water5,188288
1
BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules

BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7564
Polymers54,7102
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area6490 Å2
ΔGint-47 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.562, 65.562, 164.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11BBB-624-

HOH

21BBB-688-

HOH

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Components

#1: Protein Type-1Aa cytolytic delta-endotoxin / 27 kDa cytolytic toxin


Mass: 27354.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Structure solved from in vivo grown nanocrystals of Cyt1Aa soaked with 1mM DTT at pH 7 and room-temperature.
Source: (gene. exp.) Bacillus thuringiensis subsp. israelensis (bacteria)
Gene: cyt1Aa, cytA
Production host: Bacillus thuringiensis serovar israelensis (bacteria)
Variant (production host): 4Q7 / References: UniProt: P0A382
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 35.4 % / Description: bipyramidal crystals.
Crystal growTemperature: 300 K / Method: in cell
Details: In cell crystallization by recombinant expression in a Bacillus thuringiensis serovar israelensis strain devoid of its pBt plasmid.

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.28 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 18261 / % possible obs: 99.9 % / Redundancy: 160.5 % / CC1/2: 0.998 / R split: 0.074 / Net I/σ(I): 32.8
Reflection shellResolution: 1.83→1.85 Å / Redundancy: 30.8 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1003 / CC1/2: 0.164 / R split: 0.517 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.7 µm2 / Pulse duration: 40 fsec. / Pulse energy: 1000 µJ / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: MESH
Serial crystallography data reductionFrames indexed: 18766 / Frames total: 39547 / Lattices indexed: 18882

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Processing

Software
NameVersionClassification
REFMAC5.8.0230 2018/03/05refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6t14

6t14


Resolution: 1.85→14.838 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2901 921 -
Rwork0.2241 17339 -
all0.227 --
obs-18260 97.767 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 32.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.008 Å20.004 Å20 Å2
2--0.008 Å20 Å2
3----0.026 Å2
Refinement stepCycle: LAST / Resolution: 1.85→14.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 1 291 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0141981
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171807
X-RAY DIFFRACTIONr_angle_refined_deg0.7991.6482719
X-RAY DIFFRACTIONr_angle_other_deg1.3821.6284230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.02726.29289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73415330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.753153
X-RAY DIFFRACTIONr_chiral_restr0.0580.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022241
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02347
X-RAY DIFFRACTIONr_nbd_refined0.1860.2355
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.21631
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2940
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2159
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.238
X-RAY DIFFRACTIONr_nbd_other0.190.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.287
X-RAY DIFFRACTIONr_mcbond_it1.0783.1611009
X-RAY DIFFRACTIONr_mcbond_other1.0783.161008
X-RAY DIFFRACTIONr_mcangle_it1.8364.7461273
X-RAY DIFFRACTIONr_mcangle_other1.8354.7471274
X-RAY DIFFRACTIONr_scbond_it1.1033.246970
X-RAY DIFFRACTIONr_scbond_other1.1023.246970
X-RAY DIFFRACTIONr_scangle_it1.774.8321446
X-RAY DIFFRACTIONr_scangle_other1.774.8321446
X-RAY DIFFRACTIONr_lrange_it6.03839.3342191
X-RAY DIFFRACTIONr_lrange_other5.45837.722116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.85-1.8970.541650.4561231132198.10750.437
1.897-1.9480.457650.4061206129498.22260.382
1.948-2.0040.459620.3591156125297.28430.327
2.004-2.0640.377590.3261141123597.1660.286
2.064-2.1310.389590.3061101118597.89030.27
2.131-2.2040.402550.2961055113997.45390.254
2.204-2.2850.331550.2661037112597.06670.224
2.285-2.3760.289540.253993107897.12430.212
2.376-2.4790.321520.254964103897.88050.212
2.479-2.5960.333490.261931100897.22220.212
2.596-2.7320.293470.23488094797.88810.19
2.732-2.8920.246460.20684290897.79740.16
2.892-3.0830.255420.18379985598.36260.144
3.083-3.3180.239400.17876581698.6520.139
3.318-3.6170.222380.17471275998.81420.142
3.617-4.0140.27340.17665368899.85470.141
4.014-4.5790.199320.155976291000.123
4.579-5.480.183280.1515295571000.126
5.48-7.2690.342220.2354334551000.2
7.269-14.8380.258170.17531433299.69880.147

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