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

ID or keywords:

Entry

Database: PDB / ID: 8yqh

Title

Crystal structure of Cry3Aa-PEI at 3.1 A

Components

Cry3Aa protein

Keywords

TOXIN / 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

Biological species

Bacillus thuringiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.11 Å

Authors

Li, J. / Chan, M.K.

Funding support

Hong Kong, 2items

Citation

Journal: 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

Deposition	Mar 19, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8yqh.cif.gz	129.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8yqh.ent.gz	98.8 KB	Display	PDB format
PDBx/mmJSON format	8yqh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8yqh_validation.pdf.gz	431.4 KB	Display	wwPDB validaton report
Full document	8yqh_full_validation.pdf.gz	438.7 KB	Display
Data in XML	8yqh_validation.xml.gz	24.8 KB	Display
Data in CIF	8yqh_validation.cif.gz	32.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yq/8yqh ftp://data.pdbj.org/pub/pdb/validation_reports/yq/8yqh	HTTPS FTP

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Related structure data

Related structure data	1dlcS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cry3Aa protein

73.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

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 number	20
Space group name H-M	C222₁

#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 modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.86 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: TPS 05A / Wavelength: 1 Å

Detector

Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 26, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.1→20 Å / Num. obs: 15017 / % possible obs: 99.9 % / Redundancy: 13 % / CC_1/2: 0.98 / CC star: 0.995 / R_merge(I) obs: 0.194 / R_pim(I) all: 0.056 / R_rim(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 (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.1-3.15	13.3	0.836	752	0.837	0.955	0.236	0.869	0.428	100
3.15-3.21	12.8	0.756	739	0.86	0.962	0.219	0.788	0.435	99.6
3.21-3.27	12.3	0.62	744	0.894	0.972	0.184	0.647	0.443	99.9
3.27-3.34	12.8	0.522	722	0.938	0.984	0.151	0.544	0.476	99.6
3.34-3.41	13.2	0.652	752	0.917	0.978	0.187	0.679	0.639	99.9
3.41-3.49	12.5	0.605	722	0.979	0.995	0.186	0.634	1.247	99.7
3.49-3.58	14.1	0.364	735	0.969	0.992	0.099	0.377	0.586	100
3.58-3.67	12.9	0.448	759	0.939	0.984	0.129	0.467	1.229	99.9
3.67-3.78	13.6	0.326	733	0.982	0.995	0.091	0.339	0.652	100
3.78-3.9	12.4	0.356	744	0.972	0.993	0.108	0.372	1.444	99.6
3.9-4.04	13.1	0.227	748	0.989	0.997	0.065	0.236	0.665	100
4.04-4.2	13.7	0.163	742	0.992	0.998	0.045	0.17	0.646	100
4.2-4.39	13.5	0.133	749	0.995	0.999	0.037	0.138	0.702	100
4.39-4.62	13.1	0.116	766	0.996	0.999	0.033	0.12	0.757	100
4.62-4.9	12.9	0.106	745	0.996	0.999	0.031	0.111	0.731	100
4.9-5.27	11.6	0.106	754	0.996	0.999	0.032	0.111	0.7	100
5.27-5.79	12.8	0.106	762	0.997	0.999	0.031	0.11	0.645	99.7
5.79-6.61	12.7	0.102	761	0.996	0.999	0.029	0.106	0.671	100
6.61-8.23	13.1	0.076	779	0.998	0.999	0.022	0.079	0.761	100
8.23-20	13.3	0.054	809	0.998	1	0.016	0.057	0.968	100

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Processing

Software

Name	Version	Classification
PHENIX	(1.18_3861)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2754	814	5.43 %
R_work	0.1926	-	-
obs	0.197	14992	99.48 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.11→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4690	0	0	4	4694

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4820
X-RAY DIFFRACTION	f_angle_d	1.274	6555
X-RAY DIFFRACTION	f_dihedral_angle_d	10.138	644
X-RAY DIFFRACTION	f_chiral_restr	0.063	707
X-RAY DIFFRACTION	f_plane_restr	0.007	848

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.11-3.3	0.2976	118	0.2181	2298	X-RAY DIFFRACTION	98
3.3-3.55	0.3015	148	0.2341	2325	X-RAY DIFFRACTION	100
3.55-3.91	0.3717	125	0.2319	2343	X-RAY DIFFRACTION	100
3.91-4.47	0.234	134	0.1827	2377	X-RAY DIFFRACTION	100
4.47-5.61	0.2507	142	0.1641	2372	X-RAY DIFFRACTION	100
5.61-19.87	0.2548	147	0.1736	2463	X-RAY DIFFRACTION	100

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