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- PDB-5foz: De novo structure of the binary mosquito larvicide BinAB at pH 10 -

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Basic information

Entry
Database: PDB / ID: 5foz
TitleDe novo structure of the binary mosquito larvicide BinAB at pH 10
Components
  • LARVICIDAL TOXIN PROTEIN
  • TOXIN
KeywordsTOXIN / BINAB INSECTICIDAL TOXIN / PORE FORMING TOXIN / XFEL / SERIAL FEMTOSECOND CRYSTALLOGRAPHY / DE NOVO MIRAS PHASING / IN VIVO CRYSTALS
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / toxin activity
Similarity search - Function
Insecticidal crystal toxin / Insecticidal Crystal Toxin, P42 / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Binary larvicide subunit BinA / Binary larvicide subunit BinB
Similarity search - Component
Biological speciesLYSINIBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsColletier, J.P. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Boutet, S. / Williams, G.J. / Messerschmidt, M. ...Colletier, J.P. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / DePonte, D.P. / Sierra, R.G. / Laksmono, H. / Koglin, J.E. / Hunter, M.S. / W Park, H. / Uervirojnangkoorn, M. / Bideshi, D.L. / Brunger, A.T. / Federici, B.A. / Sauter, N.K. / Eisenberg, D.S.
CitationJournal: Nature / Year: 2016
Title: De Novo Phasing with X-Ray Laser Reveals Mosquito Larvicide Binab Structure.
Authors: Colletier, J. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Hice, R.H. / Coquelle, N. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / ...Authors: Colletier, J. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Hice, R.H. / Coquelle, N. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / Deponte, D.P. / Sierra, R.G. / Laksmono, H. / Koglin, J.E. / Hunter, M.S. / Park, H. / Uervirojnangkoorn, M. / Bideshi, D.K. / Brunger, A.T. / Federici, B.A. / Sauter, N.K. / Eisenberg, D.S.
History
DepositionNov 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.4Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs ..._reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_redundancy
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOXIN
B: LARVICIDAL TOXIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4653
Polymers93,4422
Non-polymers231
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-13.8 kcal/mol
Surface area34750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.670, 97.286, 127.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TOXIN / / TOXIC COMPONENT OF BINARY TOXIN BINAB


Mass: 41955.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: 2362 / Description: NATURALLY OCCURRING NANO-CRYSTALS / Plasmid: BTI4Q7-PPHSP-1
Production host: BACILLUS THURINGIENSIS SEROVAR ISRAELENSIS (bacteria)
Strain (production host): 4Q7 / References: UniProt: P06575
#2: Protein LARVICIDAL TOXIN PROTEIN / RECEPTOR BINDING COMPONENT OF BINARY TOXIN BINAB


Mass: 51486.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: 2362 / Description: NATURALLY OCCURRING NANO-CRYSTALS / Plasmid: BTI4Q7-PPHSP-1
Production host: BACILLUS THURINGIENSIS SEROVAR ISRAELENSIS (bacteria)
Strain (production host): 4Q7 / References: UniProt: P10565
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsONLY RESIDUES 5-370 ARE DEFINED IN THE ELECTRON DENSITY ONLY RESIDUES 28-448 ARE DEFINED IN THE ...ONLY RESIDUES 5-370 ARE DEFINED IN THE ELECTRON DENSITY ONLY RESIDUES 28-448 ARE DEFINED IN THE ELECTRON DENSITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.4 % / Description: NONE
Crystal growpH: 10
Details: NATURALLY OCCURRING NANOCRYSTALS FORMED IN VIVO, pH 10

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Data collection

DiffractionMean temperature: 287 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.459 / Wavelength: 1.459 Å
DetectorType: PIXEL ARRAY DETECTOR CSPAD / Detector: PIXEL / Date: Feb 13, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.3→43.3 Å / Num. obs: 6542289 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 88.8 % / Biso Wilson estimate: 44.61 Å2 / CC1/2: 0.973 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 19.2 % / Mean I/σ(I) obs: 5.3 / CC1/2: 0.341 / % possible all: 99.9

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Processing

Software
NameClassification
cctbx.xfeldata reduction
cctbx.primedata scaling
SHELXDphasing
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FOY

5foy


Resolution: 2.4→24.045 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 2000 4.7 %
Rwork0.1645 --
obs0.1667 42816 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→24.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6315 0 1 718 7034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026511
X-RAY DIFFRACTIONf_angle_d0.6118858
X-RAY DIFFRACTIONf_dihedral_angle_d11.3172417
X-RAY DIFFRACTIONf_chiral_restr0.025971
X-RAY DIFFRACTIONf_plane_restr0.0031158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.460.31061410.26242882X-RAY DIFFRACTION100
2.46-2.52650.31081400.24612842X-RAY DIFFRACTION100
2.5265-2.60070.2841420.2342897X-RAY DIFFRACTION100
2.6007-2.68460.29241400.23322868X-RAY DIFFRACTION100
2.6846-2.78040.33541420.21972890X-RAY DIFFRACTION100
2.7804-2.89150.26561420.20752891X-RAY DIFFRACTION100
2.8915-3.02290.24891410.19512903X-RAY DIFFRACTION100
3.0229-3.18190.24531410.18662881X-RAY DIFFRACTION100
3.1819-3.38080.23441430.16922897X-RAY DIFFRACTION100
3.3808-3.6410.1921430.1492920X-RAY DIFFRACTION100
3.641-4.00590.17491440.13382926X-RAY DIFFRACTION100
4.0059-4.58210.15811430.11742943X-RAY DIFFRACTION100
4.5821-5.75980.16871470.12852977X-RAY DIFFRACTION100
5.7598-24.0460.19471510.16873099X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 38.242 Å / Origin y: 37.5893 Å / Origin z: 13.547 Å
111213212223313233
T0.3313 Å20.0159 Å2-0.0104 Å2-0.3291 Å2-0.0104 Å2--0.2975 Å2
L0.2913 °20.1149 °20.0051 °2-0.5399 °20.0861 °2--0.3452 °2
S0.0092 Å °-0.0028 Å °0.0101 Å °0.0113 Å °0.0073 Å °0.0046 Å °-0.045 Å °0.0025 Å °-0.0193 Å °
Refinement TLS groupSelection details: ALL

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