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- PDB-6dfp: Crystal Structure of a Tripartite Toxin Component VCA0883 from Vi... -

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Basic information

Entry
Database: PDB / ID: 6dfp
TitleCrystal Structure of a Tripartite Toxin Component VCA0883 from Vibrio cholerae
ComponentsVCA0883
KeywordsOXIDOREDUCTASE / tripartite toxin / alpha-fold / putative membrane protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyHemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / membrane / Non-hemolytic enterotoxin lytic component L1
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Bacteriol. / Year: 2022
Title: A Genomic Island of Vibrio cholerae Encodes a Three-Component Cytotoxin with Monomer and Protomer Forms Structurally Similar to Alpha-Pore-Forming Toxins.
Authors: Herrera, A. / Kim, Y. / Chen, J. / Jedrzejczak, R. / Shukla, S. / Maltseva, N. / Joachimiak, G. / Welk, L. / Wiersum, G. / Jaroszewski, L. / Godzik, A. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 13, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VCA0883


Theoretical massNumber of molelcules
Total (without water)39,7231
Polymers39,7231
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.564, 37.491, 73.343
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VCA0883


Mass: 39722.891 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_A0883 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 magic / References: UniProt: Q9KL64
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 34.3 % (w/v) PEG 5000 MME, 150 mM AMPD/Tris pH 9.0, 30 mM Sodium Potassium Tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 54059 / % possible obs: 96.8 % / Redundancy: 3.8 % / CC1/2: 0.805 / Rmerge(I) obs: 0.054 / Net I/σ(I): 39
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.605 / Num. unique obs: 1960 / % possible all: 71.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→24.372 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2
RfactorNum. reflection% reflection
Rfree0.1951 2711 5.02 %
Rwork0.159 --
obs0.1608 54011 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 0 355 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063021
X-RAY DIFFRACTIONf_angle_d0.6994155
X-RAY DIFFRACTIONf_dihedral_angle_d17.6781105
X-RAY DIFFRACTIONf_chiral_restr0.065496
X-RAY DIFFRACTIONf_plane_restr0.004561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4991-1.52630.3239910.22071901X-RAY DIFFRACTION69
1.5263-1.55570.2391000.21492258X-RAY DIFFRACTION80
1.5557-1.58740.29851250.18782482X-RAY DIFFRACTION90
1.5874-1.62190.21511580.17162743X-RAY DIFFRACTION100
1.6219-1.65970.23681410.16512760X-RAY DIFFRACTION100
1.6597-1.70120.23211590.15992775X-RAY DIFFRACTION100
1.7012-1.74710.2581480.15552773X-RAY DIFFRACTION100
1.7471-1.79850.20861340.15352780X-RAY DIFFRACTION100
1.7985-1.85660.26421510.15522761X-RAY DIFFRACTION100
1.8566-1.92290.22551670.15652761X-RAY DIFFRACTION100
1.9229-1.99990.20591450.14712805X-RAY DIFFRACTION100
1.9999-2.09080.18841360.14142819X-RAY DIFFRACTION100
2.0908-2.2010.20691480.14072784X-RAY DIFFRACTION100
2.201-2.33880.17511390.1442819X-RAY DIFFRACTION100
2.3388-2.51920.20071800.15072756X-RAY DIFFRACTION100
2.5192-2.77240.22861440.17042795X-RAY DIFFRACTION100
2.7724-3.17280.1951540.17322842X-RAY DIFFRACTION100
3.1728-3.99460.17691290.15852839X-RAY DIFFRACTION100
3.9946-24.37480.15891620.15842847X-RAY DIFFRACTION97

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