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- PDB-8yqh: Crystal structure of Cry3Aa-PEI at 3.1 A -

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Basic information

Entry
Database: PDB / ID: 8yqh
TitleCrystal structure of Cry3Aa-PEI at 3.1 A
ComponentsCry3Aa protein
KeywordsTOXIN / Bacillus thuringiensis / crystal protein / insecticidal protein
Function / homology
Function and homology information


symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / signaling receptor binding / membrane
Similarity search - Function
Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal / delta endotoxin / Pesticidal crystal protein / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Crystaline entomocidal protoxin
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsLi, J. / Chan, M.K.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
Other governmentCUHK Idea Booster Fund IDBF23SCI18 Hong Kong
Other governmentHong Kong Research Grants Council GRF 14323216 Hong Kong
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Mechanoresponsive Protein Crystals for NADH Recycling in Multicycle Enzyme Reactions.
Authors: Yekta, R. / Xiong, X. / Li, J. / Heater, B.S. / Lee, M.M. / Chan, M.K.
History
DepositionMar 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cry3Aa protein


Theoretical massNumber of molelcules
Total (without water)73,1771
Polymers73,1771
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.846, 133.368, 105.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cry3Aa protein / Pesticidal protein


Mass: 73177.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry3Aa, EEL55_22485 / Production host: Bacillus thuringiensis (bacteria) / References: UniProt: Q9S6N9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Cry3Aa crystals obatined in conditon: 100 mM HEPES/NaOH pH7.5, 20% v/v 1,4-butanediol, 200 mM NaCl. Then the Cry3Aa crystals soaked with 50ug/ml PEI, 5mM EDC and 10 mM NHS at 291K overnight.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 15017 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.056 / Rrim(I) all: 0.202 / Χ2: 0.74 / Net I/σ(I): 3.8 / Num. measured all: 194996
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.1513.30.8367520.8370.9550.2360.8690.428100
3.15-3.2112.80.7567390.860.9620.2190.7880.43599.6
3.21-3.2712.30.627440.8940.9720.1840.6470.44399.9
3.27-3.3412.80.5227220.9380.9840.1510.5440.47699.6
3.34-3.4113.20.6527520.9170.9780.1870.6790.63999.9
3.41-3.4912.50.6057220.9790.9950.1860.6341.24799.7
3.49-3.5814.10.3647350.9690.9920.0990.3770.586100
3.58-3.6712.90.4487590.9390.9840.1290.4671.22999.9
3.67-3.7813.60.3267330.9820.9950.0910.3390.652100
3.78-3.912.40.3567440.9720.9930.1080.3721.44499.6
3.9-4.0413.10.2277480.9890.9970.0650.2360.665100
4.04-4.213.70.1637420.9920.9980.0450.170.646100
4.2-4.3913.50.1337490.9950.9990.0370.1380.702100
4.39-4.6213.10.1167660.9960.9990.0330.120.757100
4.62-4.912.90.1067450.9960.9990.0310.1110.731100
4.9-5.2711.60.1067540.9960.9990.0320.1110.7100
5.27-5.7912.80.1067620.9970.9990.0310.110.64599.7
5.79-6.6112.70.1027610.9960.9990.0290.1060.671100
6.61-8.2313.10.0767790.9980.9990.0220.0790.761100
8.23-2013.30.0548090.99810.0160.0570.968100

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Processing

Software
NameVersionClassification
PHENIX(1.18_3861)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLC

1dlc


Resolution: 3.11→19.87 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 814 5.43 %
Rwork0.1926 --
obs0.197 14992 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 0 4 4694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014820
X-RAY DIFFRACTIONf_angle_d1.2746555
X-RAY DIFFRACTIONf_dihedral_angle_d10.138644
X-RAY DIFFRACTIONf_chiral_restr0.063707
X-RAY DIFFRACTIONf_plane_restr0.007848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.30.29761180.21812298X-RAY DIFFRACTION98
3.3-3.550.30151480.23412325X-RAY DIFFRACTION100
3.55-3.910.37171250.23192343X-RAY DIFFRACTION100
3.91-4.470.2341340.18272377X-RAY DIFFRACTION100
4.47-5.610.25071420.16412372X-RAY DIFFRACTION100
5.61-19.870.25481470.17362463X-RAY DIFFRACTION100

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