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- PDB-7y79: Crystal structure of Cry78Aa -

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Basic information

Entry
Database: PDB / ID: 7y79
TitleCrystal structure of Cry78Aa
ComponentsToxin
KeywordsTOXIN / Cry78Aa / plant hopper
Function / homologyInsecticidal crystal toxin / Insecticidal Crystal Toxin, P42 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Ricin B, lectin domain / Ricin B-like lectins / toxin activity / Toxin
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsCao, B.B. / Nie, Y.F. / Wang, N.C. / Guan, Z.Y. / Zhang, D.L. / Zhang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770878 China
CitationJournal: Commun Biol / Year: 2022
Title: The crystal structure of Cry78Aa from Bacillus thuringiensis provides insights into its insecticidal activity.
Authors: Cao, B. / Nie, Y. / Guan, Z. / Chen, C. / Wang, N. / Wang, Z. / Shu, C. / Zhang, J. / Zhang, D.
History
DepositionJun 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin
B: Toxin


Theoretical massNumber of molelcules
Total (without water)48,0602
Polymers48,0602
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.958, 75.995, 89.028
Angle α, β, γ (deg.)90.000, 111.419, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Toxin


Mass: 24030.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3S6Q0Y2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, PEG3350, magnesium nitrate / PH range: 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.32→45 Å / Num. obs: 17763 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Net I/σ(I): 13.6
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1742 / CC1/2: 0.84 / Rpim(I) all: 0.298 / Rrim(I) all: 0.782 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→28.01 Å / SU ML: 0.3547 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.8632
RfactorNum. reflection% reflection
Rfree0.2492 847 4.77 %
Rwork0.1982 16900 -
obs0.2008 17747 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.8 Å2
Refinement stepCycle: LAST / Resolution: 2.32→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 0 85 3188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773177
X-RAY DIFFRACTIONf_angle_d0.84854316
X-RAY DIFFRACTIONf_chiral_restr0.052480
X-RAY DIFFRACTIONf_plane_restr0.0057553
X-RAY DIFFRACTIONf_dihedral_angle_d5.33331920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.470.34641310.26532782X-RAY DIFFRACTION98.35
2.47-2.660.2971370.25832813X-RAY DIFFRACTION99.93
2.66-2.920.32381470.25022800X-RAY DIFFRACTION99.86
2.92-3.350.29181230.22772840X-RAY DIFFRACTION99.9
3.35-4.210.25161740.17792792X-RAY DIFFRACTION99.83
4.21-28.010.18731350.16172873X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: 9.65991354125 Å / Origin y: 5.06173900144 Å / Origin z: 21.1081202049 Å
111213212223313233
T0.343598435781 Å20.0068799778054 Å20.0069028546549 Å2-0.379465886198 Å20.0625738397639 Å2--0.309312103991 Å2
L0.61217876842 °2-0.0610855892779 °20.34830668741 °2-0.59897793768 °20.282802360999 °2--1.0669246057 °2
S0.0414244163539 Å °0.018371652578 Å °-0.000189821813003 Å °0.0715658924173 Å °0.0634515005962 Å °0.0234928457463 Å °0.0981927937472 Å °-0.0345057663672 Å °-0.107713395634 Å °
Refinement TLS groupSelection details: all

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