PDB-9buv: Crystal structure of Cry1Fa R226Q

ID or keywords:

Entry

Database: PDB / ID: 9buv

Title

Crystal structure of Cry1Fa R226Q

Components

Pesticidal crystal protein Cry1Fa

Keywords

TOXIN

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
Similarity search - Function

Biological species

Bacillus thuringiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.024 Å

Authors

Poland, B.W. / Kakani, K. / Yamamoto, T.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Cry1Fa R226Q
Authors: Poland, B.W. / Kakani, K. / Yamamoto, T.

History

Deposition	May 17, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9buv.cif.gz	147.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9buv.ent.gz	102.7 KB	Display	PDB format
PDBx/mmJSON format	9buv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9buv_validation.pdf.gz	433.3 KB	Display	wwPDB validaton report
Full document	9buv_full_validation.pdf.gz	438.5 KB	Display
Data in XML	9buv_validation.xml.gz	22.9 KB	Display
Data in CIF	9buv_validation.cif.gz	33.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bu/9buv ftp://data.pdbj.org/pub/pdb/validation_reports/bu/9buv	HTTPS FTP

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Related structure data

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: Pesticidal crystal protein Cry1Fa

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.230, 68.350, 121.810
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pesticidal crystal protein Cry1Fa / 134 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryIF(a) Mass: 133733.484 Da / Num. of mol.: 1 / Mutation: R226Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry1Fa, cryIF, cryIF(a) / Production host: Escherichia coli (E. coli) / References: UniProt: Q03746
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Pesticidal crystal protein Cry1Fa / 134 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryIF(a)

Mass: 133733.484 Da / Num. of mol.: 1 / Mutation: R226Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus thuringiensis (bacteria) / Gene: cry1Fa, cryIF, cryIF(a) / Production host:

Escherichia coli (E. coli) / References: UniProt: Q03746

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1 Å³/Da / Density % sol: 40.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG6000, 5% MPD, 0.1 M HEPES, pH 7.5, 4% Benzamidine HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.987 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.02→68.22 Å / Num. obs: 36045 / % possible obs: 100 % / Redundancy: 11.8 % / CC_1/2: 0.993 / R_merge(I) obs: 0.126 / Net I/σ(I): 15.3
Reflection shell	Resolution: 2.02→2.13 Å / R_merge(I) obs: 0.192 / Num. unique obs: 5186 / CC_1/2: 0.983

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.024→60.905 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.928 / SU B: 3.14 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1971	1789	5.011 %	RANDOM
R_work	0.154	33909	-	-
all	0.156	-	-	-
obs	-	35698	99.997 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 15.441 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.242 Å²	0 Å²	-0 Å²
2-	-	-0.582 Å²	0 Å²
3-	-	-	-0.66 Å²

Refinement step

Cycle: LAST / Resolution: 2.024→60.905 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4567	0	0	233	4800

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.011	4687
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4307
X-RAY DIFFRACTION	r_angle_refined_deg	1.553	1.65	6398
X-RAY DIFFRACTION	r_angle_other_deg	0.537	1.561	9835
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.191	5	572
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.56	5	44
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.999	10	709
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.748	10	236
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	711
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5686
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1234
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	894
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	4045
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	2392
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2530
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	235
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.191	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.249	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.177	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	1.496	1.453	2291
X-RAY DIFFRACTION	r_mcbond_other	1.495	1.453	2291
X-RAY DIFFRACTION	r_mcangle_it	2.32	2.604	2862
X-RAY DIFFRACTION	r_mcangle_other	2.321	2.604	2863
X-RAY DIFFRACTION	r_scbond_it	2.51	1.726	2396
X-RAY DIFFRACTION	r_scbond_other	2.51	1.727	2397
X-RAY DIFFRACTION	r_scangle_it	3.891	3.029	3536
X-RAY DIFFRACTION	r_scangle_other	3.89	3.03	3537
X-RAY DIFFRACTION	r_lrange_it	5.141	15.85	5325
X-RAY DIFFRACTION	r_lrange_other	5.129	15.668	5292

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.024-2.077	0.187	113	0.137	2492	0.139	2605	0.977	0.988	100	0.133
2.077-2.133	0.202	105	0.145	2443	0.147	2548	0.974	0.987	100	0.142
2.133-2.195	0.169	145	0.129	2281	0.132	2426	0.981	0.99	100	0.128
2.195-2.263	0.183	125	0.136	2269	0.139	2394	0.98	0.989	100	0.136
2.263-2.337	0.2	112	0.144	2225	0.146	2337	0.978	0.987	100	0.144
2.337-2.419	0.206	102	0.141	2139	0.144	2241	0.975	0.987	100	0.143
2.419-2.51	0.194	107	0.146	2080	0.148	2187	0.977	0.987	100	0.148
2.51-2.612	0.211	104	0.16	1988	0.163	2092	0.971	0.984	100	0.164
2.612-2.728	0.227	110	0.161	1900	0.165	2010	0.971	0.983	100	0.165
2.728-2.861	0.22	93	0.163	1850	0.166	1943	0.972	0.983	100	0.171
2.861-3.015	0.236	112	0.166	1725	0.17	1837	0.967	0.982	100	0.176
3.015-3.198	0.193	78	0.15	1661	0.151	1739	0.977	0.986	100	0.161
3.198-3.418	0.179	105	0.157	1553	0.159	1658	0.978	0.985	100	0.172
3.418-3.691	0.195	58	0.164	1477	0.165	1535	0.979	0.984	100	0.18
3.691-4.041	0.202	83	0.153	1358	0.156	1441	0.976	0.986	100	0.171
4.041-4.516	0.159	71	0.144	1221	0.145	1292	0.987	0.988	100	0.164
4.516-5.21	0.182	39	0.14	1113	0.142	1152	0.987	0.99	100	0.161
5.21-6.369	0.232	69	0.209	927	0.21	996	0.974	0.983	100	0.236
6.369-8.958	0.179	34	0.187	748	0.186	782	0.982	0.983	100	0.213
8.958-60.905	0.217	24	0.188	459	0.19	484	0.963	0.975	99.7934	0.309

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