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- PDB-7mjr: Vip4Da2 toxin structure -

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Basic information

Entry
Database: PDB / ID: 7mjr
TitleVip4Da2 toxin structure
ComponentsVip4Da1 protein
KeywordsTOXIN / Vegetative insecticidal protein
Function / homology
Function and homology information


protein homooligomerization / extracellular region / metal ion binding
Similarity search - Function
Fungal immunomodulatory protein Fve / : / Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Protective antigen, heptamerisation domain / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / PA14/GLEYA domain / PA14 domain profile. / Bacterial exotoxin B ...Fungal immunomodulatory protein Fve / : / Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Protective antigen, heptamerisation domain / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / PA14/GLEYA domain / PA14 domain profile. / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14 domain / PA14 / PA14 domain / Galactose-binding domain-like / Jelly Rolls / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsRydel, T.J. / Duda, D. / Zheng, M. / Henry, A.
CitationJournal: Plos One / Year: 2021
Title: Structural and functional insights into the first Bacillus thuringiensis vegetative insecticidal protein of the Vpb4 fold, active against western corn rootworm.
Authors: Kouadio, J.L. / Zheng, M. / Aikins, M. / Duda, D. / Duff, S. / Chen, D. / Zhang, J. / Milligan, J. / Taylor, C. / Mamanella, P. / Rydel, T. / Kessenich, C. / Panosian, T. / Yin, Y. / Moar, W. ...Authors: Kouadio, J.L. / Zheng, M. / Aikins, M. / Duda, D. / Duff, S. / Chen, D. / Zhang, J. / Milligan, J. / Taylor, C. / Mamanella, P. / Rydel, T. / Kessenich, C. / Panosian, T. / Yin, Y. / Moar, W. / Giddings, K. / Park, Y. / Jerga, A. / Haas, J.
History
DepositionApr 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vip4Da1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,16713
Polymers105,1821
Non-polymers98512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer by gel filtration sizing
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.517, 221.374, 154.141
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Vip4Da1 protein


Mass: 105181.984 Da / Num. of mol.: 1 / Mutation: Q530Y, E531Y, K532Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: vip4Da1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: A0A2U5FTM5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 4.77 Å3/Da / Density % sol: 74.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals were obtained in 0.1 M Bis-Tris at pH 6.5, 1.8 M ammonium sulfate, and 2% (w/v) PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.22→43.05 Å / Num. obs: 31927 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 92 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.162 / Χ2: 2.065 / Net I/σ(I): 23.3
Reflection shellResolution: 3.22→3.36 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.077 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 1564 / CC1/2: 0.742 / Χ2: 0.802 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Vip4

Resolution: 3.22→43.05 Å / SU ML: 0.3794 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.3071
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2414 1926 6.27 %
Rwork0.1963 28788 -
obs0.1992 30714 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.09 Å2
Refinement stepCycle: LAST / Resolution: 3.22→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7125 0 48 0 7173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01127320
X-RAY DIFFRACTIONf_angle_d1.30729927
X-RAY DIFFRACTIONf_chiral_restr0.06711074
X-RAY DIFFRACTIONf_plane_restr0.0071274
X-RAY DIFFRACTIONf_dihedral_angle_d8.2592965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.30.287810.29061205X-RAY DIFFRACTION55.1
3.3-3.390.35761260.27431903X-RAY DIFFRACTION89.11
3.39-3.490.3371440.25531987X-RAY DIFFRACTION91.46
3.49-3.610.31240.25782032X-RAY DIFFRACTION93.25
3.61-3.740.32381300.22752047X-RAY DIFFRACTION94.78
3.74-3.890.30571370.21552097X-RAY DIFFRACTION95.76
3.89-4.060.25451510.20162118X-RAY DIFFRACTION97.55
4.06-4.280.26941470.19072125X-RAY DIFFRACTION98.18
4.28-4.540.23191310.17332184X-RAY DIFFRACTION98.93
4.54-4.890.20061550.16522169X-RAY DIFFRACTION99.06
4.89-5.390.21671420.17292190X-RAY DIFFRACTION99.57
5.39-6.160.23751480.18262207X-RAY DIFFRACTION99.66
6.16-7.760.24241510.1952228X-RAY DIFFRACTION99.71
7.76-43.050.19031590.18552296X-RAY DIFFRACTION98.95

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