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- PDB-8bad: Tpp80Aa1 -

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Basic information

Entry
Database: PDB / ID: 8bad
TitleTpp80Aa1
ComponentsBinary toxin A-like protein
KeywordsTOXIN / Bacillus thuriengiensis / mosquito / mosquitocidal / pesticidal protein
Function / homology
Function and homology information


toxin activity / metal ion binding
Similarity search - Function
Insecticidal crystal toxin / Insecticidal Crystal Toxin, P42 / Ricin-type beta-trefoil lectin domain-like / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Binary toxin A-like protein
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsBest, H.L. / Williamson, L.J. / Rizkallah, P.J. / Berry, C. / Lloyd-Evans, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Toxins / Year: 2022
Title: The Crystal Structure of Bacillus thuringiensis Tpp80Aa1 and Its Interaction with Galactose-Containing Glycolipids.
Authors: Best, H.L. / Williamson, L.J. / Lipka-Lloyd, M. / Waller-Evans, H. / Lloyd-Evans, E. / Rizkallah, P.J. / Berry, C.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
A: Binary toxin A-like protein
B: Binary toxin A-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3289
Polymers84,9262
Non-polymers1,4027
Water6,287349
1
A: Binary toxin A-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0684
Polymers42,4631
Non-polymers6053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Binary toxin A-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2605
Polymers42,4631
Non-polymers7974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.827, 63.853, 107.292
Angle α, β, γ (deg.)90.000, 120.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-614-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 5 - 353 / Label seq-ID: 5 - 353

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Binary toxin A-like protein


Mass: 42462.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V1G8Q1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02M sodium/potassium phosphate 0.1M Bis-tris propane 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.81→57.73 Å / Num. obs: 71433 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 29 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.128 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
1.81-1.846.70.62336134951.022.654
4.91-57.76756.42594736890.0150.04

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å53.9 Å
Translation2 Å53.9 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gp0, 5foy

3gp0

5foy


Resolution: 1.81→57.72 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 9.182 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 3513 4.9 %RANDOM
Rwork0.1789 ---
obs0.1805 67839 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.05 Å2 / Biso mean: 36.908 Å2 / Biso min: 19.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.46 Å2
2---0.92 Å2-0 Å2
3---1.06 Å2
Refinement stepCycle: final / Resolution: 1.81→57.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5643 0 91 349 6083
Biso mean--74.24 41.2 -
Num. residues----701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135913
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155314
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.6568036
X-RAY DIFFRACTIONr_angle_other_deg1.2521.57812278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8185709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3324.277318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20815966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.851520
X-RAY DIFFRACTIONr_chiral_restr0.0630.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026777
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021387
Refine LS restraints NCS

Ens-ID: 1 / Number: 11757 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.81→1.855 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.38 263 -
Rwork0.357 4908 -
obs--98.1 %
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)
12.4181-0.4618-1.08763.2454-0.43451.7325-0.0845-0.2248-0.2713-0.06140.01430.43360.228-0.10180.07030.0728-0.03570.02980.0640.01430.15025.7396-40.377620.0387
20.75881.1342-0.32233.0593-0.5250.7010.02470.0160.0941-0.3207-0.00220.191-0.1274-0.0337-0.02250.14960.0108-0.00130.0025-0.00140.020920.2952-6.99496.0336
32.779-0.10460.54841.3287-0.17232.84850.10310.1607-0.1273-0.1617-0.0179-0.0880.26570.2421-0.08520.0430.02240.00210.0336-0.01270.017237.1863-14.891928.2488
44.16731.2512-0.13681.18280.27910.57820.1828-0.30810.11930.1211-0.24520.3562-0.0111-0.22860.06240.0579-0.06650.0540.1891-0.06810.1468-0.1202-19.086139.0565
500000000000000-00.4596-0.1440.00180.2898-0.0020.606-2.229-44.82316.111
600000000000000-00.02740.02760.02540.603-0.04150.415942.709-7.51531.736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 155
2X-RAY DIFFRACTION2A156 - 373
3X-RAY DIFFRACTION3B1 - 155
4X-RAY DIFFRACTION4B156 - 373
5X-RAY DIFFRACTION5C1
6X-RAY DIFFRACTION6C2

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