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- PDB-5zi1: Crystal structure of Bacillus thuringiensis insecticidal crystal ... -

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Basic information

Entry
Database: PDB / ID: 5zi1
TitleCrystal structure of Bacillus thuringiensis insecticidal crystal protein Cry7Ca1 (wild type)
Componentsinsecticidal crystal protein Cry7Cal
KeywordsTOXIN / insecticidal crystal protein
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / : / toxin activity / signaling receptor binding
Similarity search - Function
Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, N-terminal domain / 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 Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, N-terminal domain / 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 / Delta-Endotoxin; domain 1 / Galactose-binding-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Crystaline entomocidal protoxin
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJing, X. / Gao, M. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31170123 China
CitationJournal: Protein Sci. / Year: 2019
Title: Crystal structure of Bacillus thuringiensis Cry7Ca1 toxin active against Locusta migratoria manilensis.
Authors: Jing, X. / Yuan, Y. / Wu, Y. / Wu, D. / Gong, P. / Gao, M.
History
DepositionMar 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: insecticidal crystal protein Cry7Cal
B: insecticidal crystal protein Cry7Cal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6603
Polymers137,6012
Non-polymers591
Water13,565753
1
A: insecticidal crystal protein Cry7Cal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8602
Polymers68,8011
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: insecticidal crystal protein Cry7Cal


Theoretical massNumber of molelcules
Total (without water)68,8011
Polymers68,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-15 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.261, 235.959, 69.025
Angle α, β, γ (deg.)90.000, 116.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein insecticidal crystal protein Cry7Cal


Mass: 68800.617 Da / Num. of mol.: 2 / Fragment: Cry7Cal toxin, UNP residues 55-641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / Strain (production host): M15 / References: UniProt: A9Q1Y3
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 3.34 Å3/Da / Density % sol: 63.2 % / Mosaicity: 0.589 °
Crystal growTemperature: 283 K / Method: evaporation / pH: 4.5 / Details: NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→43.54 Å / Num. obs: 79251 / % possible obs: 99.4 % / Redundancy: 3.76 % / Biso Wilson estimate: 47.54 Å2 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.143 / Χ2: 1.18 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
2.3-2.383.810.4392.179570.5111.0199.1
2.38-2.483.80.382.40.4421.0299.2
2.48-2.593.790.3182.80.3711.0599.4
2.59-2.733.780.2673.50.3111.1399.5
2.73-2.93.770.2144.20.2491.1699.5
2.9-3.123.760.1725.50.21.299.6
3.12-3.443.760.1377.40.161.2199.6
3.44-3.933.750.1169.30.1361.1699.8
3.93-4.953.720.10811.40.1271.399.7
4.95-43.543.620.08715.40.1031.5798.5

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Processing

Software
NameVersionClassification
d*TREK9.9.9.4Ddata scaling
PHENIX1.10_2155: ???refinement
PDB_EXTRACT3.22data extraction
d*TREK9.9.9.4Ddata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLC, 3EB7

1dlc

3eb7


Resolution: 2.3→40.796 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.5
RfactorNum. reflection% reflection
Rfree0.233 3969 5.01 %
Rwork0.1891 --
obs0.1913 79147 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.6 Å2 / Biso mean: 57.1714 Å2 / Biso min: 30.75 Å2
Refinement stepCycle: final / Resolution: 2.3→40.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9372 0 4 753 10129
Biso mean--57.24 59.3 -
Num. residues----1180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089627
X-RAY DIFFRACTIONf_angle_d0.8913085
X-RAY DIFFRACTIONf_chiral_restr0.0541454
X-RAY DIFFRACTIONf_plane_restr0.0061669
X-RAY DIFFRACTIONf_dihedral_angle_d17.5865694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.32810.3651310.30852644277599
2.3281-2.35750.36041380.29812677281599
2.3575-2.38850.32931410.2842664280599
2.3885-2.42130.30941370.27272653279099
2.4213-2.45580.3161450.27442700284599
2.4558-2.49250.32711150.27342691280699
2.4925-2.53140.31431590.26482657281699
2.5314-2.57290.32991310.25012702283399
2.5729-2.61730.27931370.239326642801100
2.6173-2.66490.28181480.24192684283299
2.6649-2.71610.31241390.23452665280499
2.7161-2.77150.29571370.23532717285499
2.7715-2.83180.28751320.242126632795100
2.8318-2.89770.35641290.2442732286199
2.8977-2.97010.28331470.24132674282199
2.9701-3.05040.28041440.220926872831100
3.0504-3.14010.28641360.211927112847100
3.1401-3.24140.25251430.211726982841100
3.2414-3.35720.25261460.183626662812100
3.3572-3.49160.23651520.188326902842100
3.4916-3.65040.22951570.172426992856100
3.6504-3.84270.22731340.157827142848100
3.8427-4.08320.20141560.157527022858100
4.0832-4.39820.17711580.137226652823100
4.3982-4.84010.14261460.137426932839100
4.8401-5.5390.20121430.147226962839100
5.539-6.97290.2071640.18652692285699
6.9729-40.80270.21361240.18362678280297

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