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- PDB-8hx3: crystal structure of secreted coleopteran active protein (Sip) -

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Basic information

Entry
Database: PDB / ID: 8hx3
Titlecrystal structure of secreted coleopteran active protein (Sip)
ComponentsSecreted coleopteran active protein
KeywordsTOXIN / Secreted coleopteran active protein
Function / homologyAerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Secreted coleopteran active protein
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsChen, Z. / Jiang, K. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31901943 China
CitationJournal: Pest Manag Sci / Year: 2023
Title: Structural insight into Bacillus thuringiensis Sip1Ab reveals its similarity to ETX_MTX2 family beta-pore-forming toxin.
Authors: Chen, Z. / Shi, Y. / Wang, D. / Liu, X. / Jiao, X. / Gao, X. / Jiang, K.
History
DepositionJan 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted coleopteran active protein
B: Secreted coleopteran active protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6015
Polymers72,3242
Non-polymers2763
Water3,333185
1
A: Secreted coleopteran active protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2542
Polymers36,1621
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted coleopteran active protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3463
Polymers36,1621
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.020, 233.987, 111.904
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 Secreted coleopteran active protein


Mass: 36162.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: sip / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z0MQV7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.2M sodium chloride, 0.1M Hepes PH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.28→45.54 Å / Num. obs: 30454 / % possible obs: 97.93 % / Redundancy: 1.61 % / Biso Wilson estimate: 40.79 Å2 / CC1/2: 0.988 / Net I/σ(I): 4.6
Reflection shellResolution: 2.284→2.366 Å / Num. unique obs: 2998 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
CRANK2phasing
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.28→45.54 Å / SU ML: 0.3379 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.3595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.278 1506 4.96 %
Rwork0.2396 28853 -
obs0.2415 30359 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.86 Å2
Refinement stepCycle: LAST / Resolution: 2.28→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 18 185 5297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235213
X-RAY DIFFRACTIONf_angle_d0.5637049
X-RAY DIFFRACTIONf_chiral_restr0.0438778
X-RAY DIFFRACTIONf_plane_restr0.0042906
X-RAY DIFFRACTIONf_dihedral_angle_d15.77061914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.360.42341390.36342556X-RAY DIFFRACTION97.26
2.36-2.440.37991400.34362628X-RAY DIFFRACTION99.14
2.44-2.540.37931210.32452619X-RAY DIFFRACTION99.35
2.54-2.660.37081340.31092615X-RAY DIFFRACTION99.17
2.66-2.80.37211240.3072660X-RAY DIFFRACTION99.15
2.8-2.970.34751590.32618X-RAY DIFFRACTION99.5
2.97-3.20.32611470.28332630X-RAY DIFFRACTION99.04
3.2-3.520.28561320.23532620X-RAY DIFFRACTION98.08
3.52-4.030.21991360.21242606X-RAY DIFFRACTION97.23
4.03-5.080.21241380.17632577X-RAY DIFFRACTION94.27
5.08-45.540.23251360.19652724X-RAY DIFFRACTION95.62
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)
11.802226542881.320464544220.566222505542.71041039828-1.524530192022.294691725730.0533129380235-0.034827940102-0.2341287163120.0921641317634-0.0455549303148-0.7097976578340.2520852649610.0819217912753-0.04686551100650.5644749505790.000635267260596-0.02239157411640.345299146302-0.02545889806440.41743939240523.021798768115.729658021421.7315600766
23.30542342678-1.80323196347-0.1541114752983.1230808985-0.1540753011220.682211982670.1911992769360.612591271475-0.41308393762-0.467372373718-0.318672716919-0.003175065174370.0861837558017-0.04076706694340.1297537989720.5061701926720.03432183908970.01675913089760.434351412679-0.05718342073160.32738882548813.887981266317.057696323611.5986522034
30.9861112516150.634176724740.007440012232774.798940037960.06470182656151.653707948070.06706914780860.06842178707070.267012407701-0.558621264201-0.09174624832791.112634912080.10872736943-0.2681157657440.02812959359260.333068451221-0.0167917883412-0.02704743061680.454562204161-0.002479789414080.490344522221-1.1006260696662.038371485912.6119573521
40.871020323417-0.345218898514-0.2604046170823.40855400388-0.2130987912820.7198699378360.0402411822230.14653259597-0.05980994854470.140446083702-0.06069784997290.4029872770040.0518131749553-0.08691981142990.01724536642560.312065069758-0.002688574800810.01645747020920.382340677106-0.06385924226170.2412510978915.2044922969735.453881367518.7062300318
51.39169070427-0.353356746592-0.6079915829475.73747297147-0.1103780764692.75729511687-0.149117189744-0.200176046022-0.01724854645950.5028388493580.0198913009626-0.212650760510.4252395876750.03194063045280.09227431518150.51126292570.0127605810321-0.1386020420450.4027056493940.01817441418970.435853345785-17.589331125519.4092279542-12.4711316561
62.05032625573.32784634147-0.04699388742223.804933923120.966297338148-0.4422367769450.516584669548-0.376503385755-0.5914714009940.666942864785-0.452349459279-0.8750119137090.05455038189130.0382399864818-0.08316510688680.526143618777-0.0866341569923-0.1881386918030.466919508270.09426593640260.518685157747-0.35813721198664.5618922842-11.0497751544
70.3716594641711.62499086932-0.1866749916874.63092199015-0.3429680210580.4623751720950.100316617823-0.0854975579008-0.2570079064210.205522230038-0.174682037905-0.8099744605830.1759524741110.1559456469160.05516954775740.3832385680260.0559483429087-0.09118680166710.4146819491320.0285543983040.574445524751-5.9569273178437.8207787429-16.5070702651
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 47 through 70 )AA47 - 701 - 24
22chain 'A' and (resid 71 through 140 )AA71 - 14025 - 94
33chain 'A' and (resid 141 through 252 )AA141 - 25295 - 206
44chain 'A' and (resid 253 through 363 )AA253 - 363207 - 317
55chain 'B' and (resid 47 through 140 )BC47 - 1401 - 94
66chain 'B' and (resid 141 through 252 )BC141 - 25295 - 206
77chain 'B' and (resid 253 through 363 )BC253 - 363207 - 317

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