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- PDB-6ezv: The cytotoxin MakA from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6ezv
TitleThe cytotoxin MakA from Vibrio cholerae
ComponentsNon-hemolytic enterotoxin lytic component L1
KeywordsTOXIN / cytotoxin / Vibrio cholerae / type-3 secretion / flagella
Function / homologyHemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / : / membrane / ACETATE ION / CACODYLATE ION / Non-hemolytic enterotoxin lytic component L1 / Non-hemolytic enterotoxin lytic component L1
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPersson, K. / Dongre, M. / Wai, S.N.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2013-2392 Sweden
Swedish Research Council2014-3878 Sweden
Swedish Research Council2016-05009 Sweden
Swedish cancer societyCAN/2014-831 Sweden
CitationJournal: Commun Biol / Year: 2018
Title: Flagella-mediated secretion of a novelVibrio choleraecytotoxin affecting both vertebrate and invertebrate hosts.
Authors: Dongre, M. / Singh, B. / Aung, K.M. / Larsson, P. / Miftakhova, R. / Persson, K. / Askarian, F. / Johannessen, M. / von Hofsten, J. / Persson, J.L. / Erhardt, M. / Tuck, S. / Uhlin, B.E. / Wai, S.N.
History
DepositionNov 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Non-hemolytic enterotoxin lytic component L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6586
Polymers42,2191
Non-polymers4395
Water2,414134
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint4 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.575, 36.527, 73.551
Angle α, β, γ (deg.)90.00, 91.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Non-hemolytic enterotoxin lytic component L1


Mass: 42219.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: B2J68_17335, BTY66_02270, EN12_17970, ERS013138_00148, ERS013140_03540, ERS013165_02450, ERS013166_00300, ERS013173_01009, ERS013186_00741, ERS013193_01370, ERS013200_01285, ERS013202_01074
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H6LLZ6, UniProt: Q9KL64*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.4 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium acetate, 24% (w/v) PEG 8000, 0.1 M sodium cacodylate pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.9→47.999 Å / Num. obs: 25893 / % possible obs: 94.5 % / Redundancy: 7.4 % / CC1/2: 0.987 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Rsym value: 0.079 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1666 / CC1/2: 0.85 / Rpim(I) all: 0.46 / Rrim(I) all: 0.907 / Rsym value: 0.785 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.999 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.59
RfactorNum. reflection% reflection
Rfree0.2489 1290 4.99 %
Rwork0.1954 --
obs0.1981 25871 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 25 134 2796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112689
X-RAY DIFFRACTIONf_angle_d1.0243657
X-RAY DIFFRACTIONf_dihedral_angle_d13.3241623
X-RAY DIFFRACTIONf_chiral_restr0.056449
X-RAY DIFFRACTIONf_plane_restr0.006473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97610.34861420.28162712X-RAY DIFFRACTION95
1.9761-2.0660.33241490.24732753X-RAY DIFFRACTION95
2.066-2.1750.28031470.20352720X-RAY DIFFRACTION95
2.175-2.31120.28021420.19812766X-RAY DIFFRACTION95
2.3112-2.48970.25721400.19992744X-RAY DIFFRACTION95
2.4897-2.74020.2321380.21122651X-RAY DIFFRACTION92
2.7402-3.13660.27171230.21042367X-RAY DIFFRACTION82
3.1366-3.95150.23961550.18792883X-RAY DIFFRACTION98
3.9515-48.01460.20841540.16752985X-RAY DIFFRACTION99
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)
11.67350.3638-2.45360.4596-0.42334.3793-0.1413-0.174-0.1274-0.0485-0.0486-0.10690.26390.12450.20120.17430.0099-0.01440.16330.0240.235415.26924.220329.9775
21.34030.4369-2.07440.6508-0.57184.76410.2765-0.32080.16580.1739-0.0756-0.0694-0.48330.3404-0.17050.2463-0.0421-0.01010.2592-0.04460.268313.21411.729741.1439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain X and resid 6:164)
2X-RAY DIFFRACTION2(chain X and resid 165:365)

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