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- PDB-6lh8: Structure of aerolysin-like protein (Bombina maxima) -

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Basic information

Entry
Database: PDB / ID: 6lh8
TitleStructure of aerolysin-like protein (Bombina maxima)
Componentsaerolysin-like protein
KeywordsTOXIN / pore-forming / aerolysin / amphibian / secretion
Biological speciesBombina maxima (large-webbed bell toad)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.729 Å
AuthorsBian, X.L. / Wang, Q.Q. / Li, X. / Teng, M.Q. / Zhang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31572268 China
National Natural Science Foundation of ChinaU1602225 China
National Natural Science Foundation of China31872226 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A cellular endolysosome-modulating pore-forming protein from a toad is negatively regulated by its paralog under oxidizing conditions.
Authors: Wang, Q. / Bian, X. / Zeng, L. / Pan, F. / Liu, L. / Liang, J. / Wang, L. / Zhou, K. / Lee, W. / Xiang, Y. / Li, S. / Teng, M. / Li, X. / Guo, X. / Zhang, Y.
History
DepositionDec 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: aerolysin-like protein


Theoretical massNumber of molelcules
Total (without water)17,5011
Polymers17,5011
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9160 Å2
Unit cell
Length a, b, c (Å)78.793, 78.793, 48.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

21A-377-

HOH

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Components

#1: Protein aerolysin-like protein


Mass: 17500.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombina maxima (large-webbed bell toad)
Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.2M magnesium chloride hexahydrate, 25% PEG 3350, 0.1M bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.729→41.58 Å / Num. obs: 16266 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 41.88
Reflection shellResolution: 1.729→1.76 Å / Mean I/σ(I) obs: 2.62 / Num. unique obs: 1522 / CC1/2: 0.884 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALEPACKHKL2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
REFMACCCP4irefinement
RefinementMethod to determine structure: SAD / Resolution: 1.729→41.578 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.42 / Phase error: 21.71
RfactorNum. reflection% reflection
Rfree0.2311 1628 10.01 %
Rwork0.1921 --
obs0.196 16266 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.37 Å2 / Biso mean: 32.6987 Å2 / Biso min: 15.53 Å2
Refinement stepCycle: final / Resolution: 1.729→41.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 0 177 1375
Biso mean---36.59 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.729-1.77990.31971240.2701113292
1.7799-1.83730.28171290.2357112693
1.8373-1.9030.2341280.2145118196
1.903-1.97920.25461330.205119997
1.9792-2.06930.23171330.196118997
2.0693-2.17830.20971350.1857121099
2.1783-2.31480.26711390.1923122198
2.3148-2.49350.23791330.2013122799
2.4935-2.74440.25221390.21691240100
2.7444-3.14140.26191410.19321261100
3.1414-3.95740.20751420.17781281100
3.9574-41.5780.20921520.17871371100

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