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- PDB-6vls: Structure of C-terminal fragment of Vip3A toxin -

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Basic information

Entry
Database: PDB / ID: 6vls
TitleStructure of C-terminal fragment of Vip3A toxin
ComponentsMaltose/maltodextrin-binding periplasmic protein,Vip3Aa
KeywordsTOXIN / Bacillus thuringiensis / Vip3A / biological control / mode of action / glycobiology
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...hydrolase activity, acting on glycosyl bonds / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Vegetative insecticide protein 3 / Vegetative insecticide protein 3A N terminal / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Maltose/maltodextrin-binding periplasmic protein / Vip3Aa
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJiang, K. / Zhang, Y. / Chen, Z. / Gao, X.
CitationJournal: Toxins / Year: 2020
Title: Structural and Functional Insights into the C-terminal Fragment of Insecticidal Vip3A Toxin ofBacillus thuringiensis.
Authors: Jiang, K. / Zhang, Y. / Chen, Z. / Wu, D. / Cai, J. / Gao, X.
History
DepositionJan 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
B: Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
C: Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
D: Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,66810
Polymers430,0324
Non-polymers6376
Water3,189177
1
A: Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7203
Polymers107,5081
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6142
Polymers107,5081
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6142
Polymers107,5081
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7203
Polymers107,5081
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.088, 127.884, 149.178
Angle α, β, γ (deg.)90.000, 91.380, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 21 through 416 or resid 421...
21(chain B and (resid 21 through 753 or resid 758...
31(chain C and (resid 21 through 416 or resid 421...
41(chain D and (resid 21 through 416 or resid 419...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTHRTHR(chain A and (resid 21 through 416 or resid 421...AA21 - 4162 - 397
12ASPASPTHRTHR(chain A and (resid 21 through 416 or resid 421...AA421 - 714402 - 695
13LEULEULYSLYS(chain A and (resid 21 through 416 or resid 421...AA723 - 753704 - 734
14ASPASPASNASN(chain A and (resid 21 through 416 or resid 421...AA758 - 820739 - 801
15TYRTYRLYSLYS(chain A and (resid 21 through 416 or resid 421...AA825 - 985806 - 966
21LYSLYSLYSLYS(chain B and (resid 21 through 753 or resid 758...BB21 - 7532 - 734
22ASPASPVALVAL(chain B and (resid 21 through 753 or resid 758...BB758 - 771739 - 752
23GLYGLYASNASN(chain B and (resid 21 through 753 or resid 758...BB776 - 820757 - 801
24TYRTYRLYSLYS(chain B and (resid 21 through 753 or resid 758...BB825 - 985806 - 966
31LYSLYSTHRTHR(chain C and (resid 21 through 416 or resid 421...CC21 - 4162 - 397
32ASPASPTHRTHR(chain C and (resid 21 through 416 or resid 421...CC421 - 714402 - 695
33LEULEUVALVAL(chain C and (resid 21 through 416 or resid 421...CC723 - 771704 - 752
34GLYGLYLYSLYS(chain C and (resid 21 through 416 or resid 421...CC776 - 985757 - 966
41LYSLYSTHRTHR(chain D and (resid 21 through 416 or resid 419...DD21 - 4162 - 397
42ASPASPASPASP(chain D and (resid 21 through 416 or resid 419...DD419400
43GLYGLYTHRTHR(chain D and (resid 21 through 416 or resid 419...DD422 - 714403 - 695
44GLYGLYASNASN(chain D and (resid 21 through 416 or resid 419...DD776 - 820757 - 801
45GLYGLYASNASN(chain D and (resid 21 through 416 or resid 419...DD776 - 820757 - 801
46TYRTYRLYSLYS(chain D and (resid 21 through 416 or resid 419...DD825 - 985806 - 966

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Vip3Aa


Mass: 107507.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Bacillus thuringiensis (bacteria)
Gene: malE, b4034, JW3994 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: W8GI72
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Compound detailsfusion protein consisting of MBP and residues 200 to the end of Vip3Aa
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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M sodium acetate pH 4.2, 0.5 M potassium formate, 0.1 M ammonium sulfate and 11% PEG4000
PH range: 4.0-4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.195→28.93 Å / Num. obs: 82438 / % possible obs: 97.33 % / Redundancy: 2.3 % / Biso Wilson estimate: 71.42 Å2 / CC1/2: 0.993 / Net I/σ(I): 6.11
Reflection shellResolution: 3.195→3.309 Å / Num. unique obs: 8077 / CC1/2: 0.541

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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: 3MBP

3mbp


Resolution: 3.2→28.93 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 3939 4.78 %
Rwork0.198 78409 -
obs0.2 82348 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.57 Å2 / Biso mean: 74.1403 Å2 / Biso min: 1.66 Å2
Refinement stepCycle: final / Resolution: 3.2→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29960 0 42 177 30179
Biso mean--86.7 40.48 -
Num. residues----3820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00230603
X-RAY DIFFRACTIONf_angle_d0.57241444
X-RAY DIFFRACTIONf_dihedral_angle_d18.8324082
X-RAY DIFFRACTIONf_chiral_restr0.0434630
X-RAY DIFFRACTIONf_plane_restr0.0035343
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11297X-RAY DIFFRACTION13.051TORSIONAL
12B11297X-RAY DIFFRACTION13.051TORSIONAL
13C11297X-RAY DIFFRACTION13.051TORSIONAL
14D11297X-RAY DIFFRACTION13.051TORSIONAL
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 (%)
3.2-3.230.36021480.30172428257686
3.23-3.280.35021280.30872769289796
3.28-3.320.37161440.29352771291597
3.32-3.360.34581360.27542793292998
3.36-3.410.30521220.26742844296698
3.41-3.460.28731600.24692829298998
3.46-3.520.29071690.23792756292598
3.52-3.570.26761720.23182821299398
3.57-3.640.26151490.22052774292398
3.64-3.70.29431510.2162792294398
3.7-3.770.26541350.2152835297098
3.77-3.850.22731400.21032832297298
3.85-3.930.23411190.2012813293298
3.93-4.020.2981330.19692817295097
4.02-4.120.23631220.18742823294598
4.12-4.240.21481420.17762837297998
4.24-4.360.20521250.16352833295899
4.36-4.50.20761280.15712831295998
4.5-4.660.17531210.15042863298498
4.66-4.850.1991470.14952835298299
4.85-5.070.20121360.15162838297498
5.07-5.330.18931480.1642834298298
5.33-5.660.21191360.17362861299799
5.66-6.10.23621640.18832822298699
6.1-6.70.20231510.19962870302199
6.7-7.660.24841430.2012834297798
7.66-9.590.20261190.19362880299998
9.59-28.930.22691510.20272574272587
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7063-0.9648-0.46015.3649-0.53371.4973-0.1426-0.46610.26950.89980.2267-0.5295-0.31240.3819-0.0930.5210.0562-0.14830.6426-0.08480.502219.758616.881616.8245
21.67761.0082-0.78930.9373-0.44390.588-0.0542-0.0401-0.14130.05050.035-0.18420.12330.08420.01460.3779-0.0164-0.03710.3608-0.02340.3018-47.237114.241113.6999
31.5653-0.2340.15967.6047-2.5562.1651-0.03230.3069-0.2548-0.2554-0.0808-0.36580.04980.35150.10430.3611-0.05960.02880.5205-0.11290.3153-51.16846.0525-26.0475
45.44121.261.95020.28260.44910.69170.22170.277-0.35670.0268-0.1246-0.34440.21370.1358-0.08680.48340.0469-0.03140.41750.01530.601-16.817429.4988-12.8151
56.2049-3.2193-1.3161.92531.06270.85470.41340.26740.2596-0.3857-0.2127-0.1531-0.0684-0.0149-0.20350.38570.0120.00360.34260.08670.41217.735319.5237-19.9433
68.2544-1.87641.97160.5047-0.53770.980.201-0.0672-0.1419-0.1306-0.11620.0620.1898-0.2181-0.09220.60870.01410.06350.3996-0.10310.467125.0571-4.5623-27.7933
71.9138-0.3630.03685.83841.68024.6118-0.04540.16340.5667-0.71410.0119-0.2302-1.14350.14680.02730.7057-0.0704-0.12930.56840.05960.5415119.115327.0467-94.7429
85.308-4.08430.31613.53790.78542.6529-0.0338-0.45231.00490.17180.203-0.62870.01490.2255-0.17750.4638-0.0612-0.06170.4585-0.00660.426971.91753.5664-77.8833
92.7781-1.22490.84661.8725-0.47051.6981-0.0527-0.02550.1110.0780.1013-0.0563-0.1904-0.1218-0.05940.4782-0.09660.03890.41170.03830.275751.414.9223-93.4207
103.2246-0.1342-1.50021.2354-0.54031.38660.2021-0.21730.24450.2614-0.1295-0.1787-0.37150.0692-0.07370.6643-0.0894-0.08440.48360.0190.329947.388934.2802-102.0929
117.1659-4.7199-4.39845.22826.58049.10220.55990.48020.7181-0.7576-0.2881-0.369-0.89110.1184-0.26370.6660.01160.01650.57770.1730.39446.458234.3551-69.5991
121.6098-1.1755-0.69134.8031-0.4242.117-0.0994-0.2007-0.16140.55450.09110.35190.2152-0.32830.01050.5692-0.0915-0.03170.6861-0.01040.289149.766214.5581-53.6269
138.10724.74281.73885.28361.89613.640.4964-0.2398-0.22890.4033-0.1813-0.2768-0.01250.0787-0.30190.48730.0155-0.01950.4858-0.05290.3512101.43544.5295-71.22
143.4951.1246-0.05944.6883-1.54433.55310.1526-0.2390.17010.3953-0.19890.071-0.29560.03960.02880.37550.0203-0.00710.3687-0.19060.4179123.67426.1446-53.4855
153.5497-2.3964-1.44352.42052.06023.38780.0586-0.05250.0816-0.01850.0370.0099-0.1823-0.1051-0.11090.4041-0.0288-0.03090.3623-0.01150.2995103.346434.4715-51.6386
167.96461.71170.05570.37550.008-0.0185-0.0839-0.1424-0.39470.1074-0.0199-0.2087-0.34720.12240.09680.66160.0094-0.09580.6249-0.08090.5542126.831245.8795-42.8662
179.33054.0127-0.02339.43481.06965.22270.02030.405-0.7216-0.0428-0.0041-0.1970.16110.1964-0.00420.4327-0.0146-0.15560.4322-0.02750.419152.491343.2676-49.7568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 371 )A21 - 371
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 985 )A372 - 985
3X-RAY DIFFRACTION3chain 'B' and (resid 21 through 353 )B21 - 353
4X-RAY DIFFRACTION4chain 'B' and (resid 354 through 462 )B354 - 462
5X-RAY DIFFRACTION5chain 'B' and (resid 463 through 731 )B463 - 731
6X-RAY DIFFRACTION6chain 'B' and (resid 732 through 985 )B732 - 985
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 396 )C21 - 396
8X-RAY DIFFRACTION8chain 'C' and (resid 397 through 491 )C397 - 491
9X-RAY DIFFRACTION9chain 'C' and (resid 492 through 713 )C492 - 713
10X-RAY DIFFRACTION10chain 'C' and (resid 714 through 985 )C714 - 985
11X-RAY DIFFRACTION11chain 'D' and (resid 21 through 78 )D21 - 78
12X-RAY DIFFRACTION12chain 'D' and (resid 79 through 396 )D79 - 396
13X-RAY DIFFRACTION13chain 'D' and (resid 397 through 517 )D397 - 517
14X-RAY DIFFRACTION14chain 'D' and (resid 518 through 673 )D518 - 673
15X-RAY DIFFRACTION15chain 'D' and (resid 674 through 833 )D674 - 833
16X-RAY DIFFRACTION16chain 'D' and (resid 834 through 901 )D834 - 901
17X-RAY DIFFRACTION17chain 'D' and (resid 902 through 985 )D902 - 985

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