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

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Basic information

Entry
Database: PDB / ID: 6lhz
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.52 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 China (NSFC)31572268 China
National Natural Science Foundation of China (NSFC)U1602225 China
National Natural Science Foundation of China (NSFC)31872226 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 10, 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 1.3Nov 22, 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
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
Water50428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9190 Å2
Unit cell
Length a, b, c (Å)79.082, 79.082, 48.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 43.44 % / Description: tetrahedral
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.2 M magnesium chloride hexahydrate, 25% polyethylene glycol 3350, 0.1 M Bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2018
Diffraction measurementDetails: 1.00 degrees, -1.0 sec, detector distance 249.38 mm
Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.117 / Number: 75766
ReflectionResolution: 2.52→50 Å / Num. obs: 5562 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/av σ(I): 20.532 / Net I/σ(I): 18.5
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 14 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 12.571 / Num. unique obs: 3919 / Rsym value: 0.492 / % possible all: 100
Cell measurementReflection used: 75766

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LH8

6lh8


Resolution: 2.52→36.72 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 15.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 274 4.93 %
Rwork0.1929 5288 -
obs0.1969 5562 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.47 Å2 / Biso mean: 51.1841 Å2 / Biso min: 24.07 Å2
Refinement stepCycle: final / Resolution: 2.52→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 0 28 1226
Biso mean---43.65 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.52-3.17460.37411320.19672563
3.1746-36.720.23431420.19172725

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