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- PDB-7y78: Crystal structure of Cry78Aa -

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Basic information

Entry
Database: PDB / ID: 7y78
TitleCrystal structure of Cry78Aa
ComponentsToxin
KeywordsTOXIN / Cry78Aa / plant hopper
Function / homology
Function and homology information


Insecticidal crystal toxin / Insecticidal Crystal Toxin, P42 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins
Similarity search - Domain/homology
AMMONIUM ION / Toxin
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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)2017YFD0200400 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

Downloads & links

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Assembly

Deposited unit
A: Toxin
B: Toxin
C: Toxin
D: Toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,49912
Polymers159,1784
Non-polymers3208
Water00
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)66.936, 132.741, 314.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein
Toxin


Mass: 39794.574 Da / Num. of mol.: 4
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: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.39 Å3/Da / Density % sol: 72.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, PEG3350, ammonium chloride / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 63102 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 67.16 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Net I/σ(I): 12.6
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4303 / CC1/2: 0.933 / Rpim(I) all: 0.292 / Rrim(I) all: 0.761 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→48.78 Å / SU ML: 0.4569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.0401
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2822 3152 5.01 %
Rwork0.2792 59762 -
obs0.2793 62914 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.19 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10893 0 20 0 10913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008211156
X-RAY DIFFRACTIONf_angle_d0.727115123
X-RAY DIFFRACTIONf_chiral_restr0.05561664
X-RAY DIFFRACTIONf_plane_restr0.00411972
X-RAY DIFFRACTIONf_dihedral_angle_d9.96664089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.47091330.44912490X-RAY DIFFRACTION97.84
2.94-2.990.38381370.41672509X-RAY DIFFRACTION99.03
2.99-3.040.42671460.40082579X-RAY DIFFRACTION99.16
3.04-3.090.3611340.37092559X-RAY DIFFRACTION99.56
3.09-3.150.4141330.35512524X-RAY DIFFRACTION98.55
3.15-3.210.34871170.34152601X-RAY DIFFRACTION99.67
3.21-3.270.31831430.33352518X-RAY DIFFRACTION99.85
3.27-3.340.30141380.33752632X-RAY DIFFRACTION99.89
3.34-3.420.39491380.35472553X-RAY DIFFRACTION99.93
3.42-3.510.37051280.352612X-RAY DIFFRACTION99.85
3.51-3.60.361360.33752560X-RAY DIFFRACTION99.81
3.6-3.710.32521230.30882652X-RAY DIFFRACTION99.96
3.71-3.830.28841470.29182531X-RAY DIFFRACTION99.85
3.83-3.970.29511480.26362603X-RAY DIFFRACTION99.89
3.97-4.120.25931190.2462605X-RAY DIFFRACTION99.23
4.12-4.310.23061370.23432579X-RAY DIFFRACTION99.85
4.31-4.540.21631300.22592629X-RAY DIFFRACTION99.64
4.54-4.820.2231350.20222651X-RAY DIFFRACTION99.93
4.82-5.20.17881260.21842626X-RAY DIFFRACTION99.82
5.2-5.720.25671580.25612623X-RAY DIFFRACTION99.68
5.72-6.540.26811440.26542645X-RAY DIFFRACTION99.47
6.54-8.230.26491390.26752705X-RAY DIFFRACTION99.96
8.24-48.780.27061630.27042776X-RAY DIFFRACTION98.06
Refinement TLS params.Method: refined / Origin x: -36.5170765536 Å / Origin y: 2.8201423951 Å / Origin z: -38.9462525852 Å
111213212223313233
T0.393881625818 Å20.103090680571 Å2-0.067357545528 Å2-0.451147250596 Å2-0.0944073040703 Å2--0.527276584787 Å2
L0.453726073415 °20.101118242053 °2-0.112005840926 °2-0.509229034981 °2-0.102051579599 °2--0.269258282192 °2
S-0.0922417447362 Å °0.0444572138279 Å °0.039744699541 Å °-0.0166136056962 Å °-0.0668140368864 Å °0.0552234428944 Å °0.00410264239663 Å °-0.0936124962451 Å °0.162162162355 Å °
Refinement TLS groupSelection details: all

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