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- PDB-6v1v: VIP3B (VIP3B_2160) adapted for crystallization -

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Basic information

Entry
Database: PDB / ID: 6v1v
TitleVIP3B (VIP3B_2160) adapted for crystallization
ComponentsVegetative insecticidal protein
KeywordsTOXIN / insecticidal protein Bacillus thuringiensis pore forming
Function / homologyVegetative insecticide protein 3 / Vegetative insecticide protein 3A N terminal / Vegetative insecticidal protein
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.189 Å
AuthorsEvdokimov, A.G. / Zheng, M. / Moshiri, F. / Haas, J. / Lowder, C.
CitationJournal: Protein Sci. / Year: 2020
Title: Crystal structure of a Vip3B family insecticidal protein reveals a new fold and a unique tetrameric assembly.
Authors: Zheng, M. / Evdokimov, A.G. / Moshiri, F. / Lowder, C. / Haas, J.
History
DepositionNov 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vegetative insecticidal protein
B: Vegetative insecticidal protein
C: Vegetative insecticidal protein
D: Vegetative insecticidal protein


Theoretical massNumber of molelcules
Total (without water)360,2864
Polymers360,2864
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16200 Å2
ΔGint-98 kcal/mol
Surface area127300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.488, 106.542, 117.728
Angle α, β, γ (deg.)96.130, 70.930, 69.520
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
21Chains A C
31Chains A D
41Chains B C
51Chains B D
61Chains C D

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: 1

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA22 - 79432 - 796
12GLUGLUBB22 - 79432 - 796
21LYSLYSAA22 - 79332 - 795
22LYSLYSCC22 - 79332 - 795
31GLUGLUAA22 - 79432 - 796
32GLUGLUDD22 - 79432 - 796
41GLUGLUBB22 - 79432 - 796
42GLUGLUCC22 - 79432 - 796
51GLUGLUBB22 - 79432 - 796
52GLUGLUDD22 - 79432 - 796
61GLUGLUCC22 - 79432 - 796
62GLUGLUDD22 - 79432 - 796

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Components

#1: Protein
Vegetative insecticidal protein / Vip3B2160


Mass: 90071.555 Da / Num. of mol.: 4
Mutation: E514A, K515A, Q517A, K518A, delta466..474->S, delta581..584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: vip3Bc1 / Plasmid: pET28 / Details (production host): N-terminal His-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A290WPI2

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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: 3.39 Å3/Da / Density % sol: 63.73 % / Description: prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% PEG 1500, 100 mM Bis-Tris Propane pH 9.0, 100 mM NaCl.
Temp details: incubator

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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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 16, 2014
RadiationMonochromator: Si 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.189→49.892 Å / Num. obs: 72704 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.064 / Rrim(I) all: 0.117 / Net I/σ(I): 15.2
Reflection shellResolution: 3.189→3.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.95 / Num. unique obs: 3617 / CC1/2: 0.388 / Rpim(I) all: 0.668 / Rrim(I) all: 0.95 / Χ2: 0.607 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: truncated protein (structure to be published)

Resolution: 3.189→49.892 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.922 / SU B: 27.26 / SU ML: 0.446 / Cross valid method: FREE R-VALUE / ESU R Free: 0.494
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2586 3538 4.866 %
Rwork0.218 --
all0.22 --
obs-72704 98.273 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 107.401 Å2
Baniso -1Baniso -2Baniso -3
1-1.143 Å2-2.691 Å2-0.342 Å2
2---0.801 Å2-1.076 Å2
3----0.977 Å2
Refinement stepCycle: LAST / Resolution: 3.189→49.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23683 0 0 0 23683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01324087
X-RAY DIFFRACTIONr_bond_other_d0.0020.01722313
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0670.0122880
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.63932564
X-RAY DIFFRACTIONr_angle_other_deg1.5141.57552072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9752946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1325.0411212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.598154400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8011568
X-RAY DIFFRACTIONr_chiral_restr0.0960.23252
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024626
X-RAY DIFFRACTIONr_nbd_refined0.2190.24611
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2240.221368
X-RAY DIFFRACTIONr_nbtor_refined0.180.211533
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.211706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2483
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3040.224
X-RAY DIFFRACTIONr_nbd_other0.3960.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.25
X-RAY DIFFRACTIONr_mcbond_it8.02511.40311862
X-RAY DIFFRACTIONr_mcbond_other8.02511.40311861
X-RAY DIFFRACTIONr_mcangle_it12.25117.10914782
X-RAY DIFFRACTIONr_mcangle_other12.25117.1114783
X-RAY DIFFRACTIONr_scbond_it8.03311.9912225
X-RAY DIFFRACTIONr_scbond_other8.03111.9912223
X-RAY DIFFRACTIONr_scangle_it12.64717.73917782
X-RAY DIFFRACTIONr_scangle_other12.64517.73917782
X-RAY DIFFRACTIONr_lrange_it16.959216.0241724
X-RAY DIFFRACTIONr_lrange_other16.959216.0241725
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.0523936
X-RAY DIFFRACTIONr_ncsr_local_group_20.1050.0522637
X-RAY DIFFRACTIONr_ncsr_local_group_30.1140.0522215
X-RAY DIFFRACTIONr_ncsr_local_group_40.1050.0522517
X-RAY DIFFRACTIONr_ncsr_local_group_50.110.0522092
X-RAY DIFFRACTIONr_ncsr_local_group_60.0980.0522869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.189-3.2710.3582460.3374587X-RAY DIFFRACTION88.5976
3.271-3.3610.3542510.3115028X-RAY DIFFRACTION98.7283
3.361-3.4580.3332640.2974833X-RAY DIFFRACTION98.7599
3.458-3.5650.3322420.274778X-RAY DIFFRACTION98.9163
3.565-3.6810.3152120.2534633X-RAY DIFFRACTION98.9179
3.681-3.810.2812140.2444467X-RAY DIFFRACTION98.9641
3.81-3.9540.3242020.2284291X-RAY DIFFRACTION99.0302
3.954-4.1150.2542160.24070X-RAY DIFFRACTION99.0754
4.115-4.2980.2382100.1893990X-RAY DIFFRACTION99.1501
4.298-4.5070.2091910.1743790X-RAY DIFFRACTION99.0545
4.507-4.7510.2091850.1643580X-RAY DIFFRACTION99.1311
4.751-5.0380.2082050.1573408X-RAY DIFFRACTION99.1765
5.038-5.3850.2421700.1873200X-RAY DIFFRACTION99.3807
5.385-5.8160.2791330.2213001X-RAY DIFFRACTION99.3974
5.816-6.3690.3281380.2352748X-RAY DIFFRACTION99.3802
6.369-7.1170.2751170.1992521X-RAY DIFFRACTION99.6224
7.117-8.2120.2291250.1872187X-RAY DIFFRACTION99.5265
8.212-10.0440.1981030.1811838X-RAY DIFFRACTION99.1318
10.044-14.1420.229790.2071426X-RAY DIFFRACTION99.4055
14.142-49.8920.333350.377790X-RAY DIFFRACTION96.831

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