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- PDB-6tao: The cytotoxin MakE from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6tao
TitleThe cytotoxin MakE from Vibrio cholerae
ComponentsNon-hemolytic enterotoxin lytic component L1
KeywordsTOXIN / cytotoxin cholera
Function / homology: / Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Up-down Bundle / Mainly Alpha / membrane / NICKEL (II) 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: 1.98 Å
AuthorsPersson, K. / Nagampalli, R. / Heidler, T. / Wai, S.N.
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 30, 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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,7468
Polymers78,3192
Non-polymers4276
Water7,422412
1
A: Non-hemolytic enterotoxin lytic component L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4695
Polymers39,1601
Non-polymers3104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-hemolytic enterotoxin lytic component L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2773
Polymers39,1601
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.929, 94.936, 63.636
Angle α, β, γ (deg.)90.000, 110.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Non-hemolytic enterotoxin lytic component L1


Mass: 39159.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: C9J66_02380, EC575_16750, EN12_17975, ERS013140_03541, ERS013165_02451, ERS013186_00740, ERS013198_00092, ERS013199_01996, ERS013200_01286, ERS013201_03487, ERS013202_01073, ERS013206_01275, EYB64_16860
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F4FI88, UniProt: Q9KL63*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 10 mM Nickel chloride, 0.1 M Tris pH 8.5, 20% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.98→49.175 Å / Num. obs: 44118 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.051 / Rrim(I) all: 0.11 / Net I/σ(I): 9.6
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
1.98-2.054.41.1341878942880.560.6081.2911.2100
7.67-49.174.30.03133967870.9990.0160.03635.998.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→49.175 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.46
RfactorNum. reflection% reflection
Rfree0.235 2000 4.54 %
Rwork0.1768 --
obs0.1794 44086 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.74 Å2 / Biso mean: 45.6225 Å2 / Biso min: 20.55 Å2
Refinement stepCycle: final / Resolution: 1.98→49.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 14 412 5792
Biso mean--81.22 43.05 -
Num. residues----691
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.98-2.02950.34711410.30642973100
2.0295-2.08440.33461420.26822978100
2.0844-2.14580.28641420.24382994100
2.1458-2.2150.2611430.22363021100
2.215-2.29420.25861420.21322996100
2.2942-2.3860.28561440.20413017100
2.386-2.49460.24581420.19512978100
2.4946-2.62610.25611410.19492985100
2.6261-2.79070.2691440.19253032100
2.7907-3.00610.25231450.19563021100
3.0061-3.30860.28321410.17892987100
3.3086-3.78720.22061440.15473031100
3.7872-4.77080.20031440.12593027100
4.7708-49.1750.17421450.158304699
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)
10.55990.4272-0.48471.4848-1.33662.14360.0454-0.1019-0.07140.1856-0.0488-0.0766-0.15720.07190.01080.1801-0.0063-0.01310.22040.00110.2012-0.2452-0.42737.9421
20.5863-0.6810.24513.0121-0.52880.7635-0.004-0.0986-0.05720.11170.1220.23870.0069-0.0774-0.10670.1808-0.04210.02350.23280.03240.2284-20.080416.615-14.0155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:356)A6 - 356
2X-RAY DIFFRACTION2(chain B and resid 6:356)B6 - 356

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