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- PDB-6t8d: The cytotoxin MakB from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6t8d
TitleThe cytotoxin MakB from Vibrio cholerae
ComponentsMakB
KeywordsTOXIN / cytotoxin / virulence factor
Function / homologyNon-hemolytic enterotoxin lytic component L1
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsPersson, K. / Nagampalli, R.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Swedish Research Council2018-02914 Sweden
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A tripartite cytolytic toxin formed by Vibrio cholerae proteins with flagellum-facilitated secretion.
Authors: Nadeem, A. / Nagampalli, R. / Toh, E. / Alam, A. / Myint, S.L. / Heidler, T.V. / Dongre, M. / Zlatkov, N. / Pace, H. / Bano, F. / Sjostedt, A. / Bally, M. / Uhlin, B.E. / Wai, S.N. / Persson, K.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: MakB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1213
Polymers41,9291
Non-polymers1922
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-24 kcal/mol
Surface area16830 Å2
Unit cell
Length a, b, c (Å)53.287, 54.230, 120.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MakB


Mass: 41929.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0882 / Plasmid: pET-His1a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9KL65
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.5 M MgSO4, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→120.81 Å / Num. obs: 21126 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 38.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.045 / Rrim(I) all: 0.113 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.166.50.9411097516980.8160.3991.0241.999.5
8.91-120.815.20.06516693220.990.0310.07221.997.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.11data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→60.405 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.58
RfactorNum. reflection% reflection
Rfree0.2612 1056 5.01 %
Rwork0.2154 --
obs0.2177 21070 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.79 Å2 / Biso mean: 53.7709 Å2 / Biso min: 26.8 Å2
Refinement stepCycle: final / Resolution: 2.1→60.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 10 63 2800
Biso mean--63.27 48.36 -
Num. residues----355
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.19560.30821290.27992442
2.1956-2.31130.30061310.26052459
2.3113-2.45620.26911320.25242467
2.4562-2.64580.29051280.2332466
2.6458-2.91210.35951280.25782489
2.9121-3.33340.28411310.24552511
3.3334-4.19960.27111360.19652528
4.1996-60.4050.20181410.17972652

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