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- PDB-8alo: Heterodimer formation of sensory domains of Vibrio cholerae regul... -

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Basic information

Entry
Database: PDB / ID: 8alo
TitleHeterodimer formation of sensory domains of Vibrio cholerae regulators ToxR and ToxS
Components
  • Cholera toxin transcriptional activator
  • Transmembrane regulatory protein ToxS
KeywordsMEMBRANE PROTEIN / Vibrio cholerae / transcription regulator / protein complex / ToxR / ToxS / hetero complex
Function / homology
Function and homology information


phosphorelay response regulator activity / regulation of DNA-templated transcription / DNA binding / plasma membrane
Similarity search - Function
Trans-membrane regulatory protein ToxS / Trans-membrane regulatory protein ToxS / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Cholera toxin transcriptional activator / Transmembrane regulatory protein ToxS
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsGubensaek, N. / Sagmeister, T. / Pavkov-Keller, T. / Zangger, K. / Buhlheller, C. / Wagner, G.E.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundT-1239 Austria
Citation
Journal: Elife / Year: 2023
Title: Vibrio cholerae's ToxRS bile sensing system.
Authors: Gubensak, N. / Sagmeister, T. / Buhlheller, C. / Geronimo, B.D. / Wagner, G.E. / Petrowitsch, L. / Grawert, M.A. / Rotzinger, M. / Berger, T.M.I. / Schafer, J. / Uson, I. / Reidl, J. / ...Authors: Gubensak, N. / Sagmeister, T. / Buhlheller, C. / Geronimo, B.D. / Wagner, G.E. / Petrowitsch, L. / Grawert, M.A. / Rotzinger, M. / Berger, T.M.I. / Schafer, J. / Uson, I. / Reidl, J. / Sanchez-Murcia, P.A. / Zangger, K. / Pavkov-Keller, T.
#1: Journal: Mol Microbiol / Year: 2021
Title: The periplasmic domains of Vibrio cholerae ToxR and ToxS are forming a strong heterodimeric complex independent on the redox state of ToxR cysteines.
Authors: Gubensaek, N. / Wagner, G.E. / Schrank, E. / Falsone, F.S. / Berger, T.M.I. / Pavkov-Keller, T. / Reidl, J. / Zangger, K.
History
DepositionAug 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholera toxin transcriptional activator
B: Transmembrane regulatory protein ToxS


Theoretical massNumber of molelcules
Total (without water)30,3312
Polymers30,3312
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-13 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.507, 72.507, 79.463
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cholera toxin transcriptional activator


Mass: 11649.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: toxR, VC_0984 / Production host: Escherichia coli (E. coli) / References: UniProt: P15795
#2: Protein Transmembrane regulatory protein ToxS


Mass: 18681.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: toxS, VC_0983 / Production host: Escherichia coli (E. coli) / References: UniProt: P24003
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 30mg/ml of ToxRSp in Tris buffer (20mM Tris, 150mM NaCl, pH7), 0.5 microliters of protein was mixed with 0.5 microliters of crystal condition (0.2 M Magnesium chloride hexahydrate. 0.1 M BIS- ...Details: 30mg/ml of ToxRSp in Tris buffer (20mM Tris, 150mM NaCl, pH7), 0.5 microliters of protein was mixed with 0.5 microliters of crystal condition (0.2 M Magnesium chloride hexahydrate. 0.1 M BIS-Tris. 5.5. 25 % w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3→62.793 Å / Num. obs: 4790 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.059 / Rrim(I) all: 0.123 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-62.797.60.0341830.9990.0180.039
3-3.187.80.8427560.6880.4660.966

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold Model

Resolution: 3.002→62.793 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: FREE R-VALUE / ESU R Free: 0.497
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2529 260 5.431 %
Rwork0.2129 4527 -
all0.215 --
obs-4787 99.896 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 87.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.922 Å2-0.461 Å2-0 Å2
2---0.922 Å20 Å2
3---2.991 Å2
Refinement stepCycle: LAST / Resolution: 3.002→62.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 0 11 1865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121887
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.632565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9415234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46524.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15515335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.217158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021410
X-RAY DIFFRACTIONr_nbd_refined0.2130.2659
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.249
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3420.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4280.24
X-RAY DIFFRACTIONr_mcbond_it5.6268.403942
X-RAY DIFFRACTIONr_mcangle_it8.912.5921174
X-RAY DIFFRACTIONr_scbond_it6.7248.974945
X-RAY DIFFRACTIONr_scangle_it10.55113.2121391
X-RAY DIFFRACTIONr_lrange_it14.783112.9762550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.002-3.080.339240.2993130.3023370.8280.8181000.284
3.08-3.1640.337260.273300.2753560.8070.8411000.249
3.164-3.2550.298200.2633110.2653320.8110.8699.69880.24
3.255-3.3550.29140.2333050.2353190.860.8921000.208
3.355-3.4650.243210.2383050.2393260.8640.91000.214
3.465-3.5860.296140.1962830.2012970.8960.9251000.168
3.586-3.7210.11110.1952760.1912870.9590.9271000.178
3.721-3.8720.349130.22630.2062760.8760.9251000.176
3.872-4.0440.249180.2012620.2042800.8950.9351000.178
4.044-4.240.191120.1822540.1822660.9270.9451000.162
4.24-4.4690.24150.1842410.1862470.930.9599.59510.168
4.469-4.7380.142200.1782020.1742230.9650.9599.55160.166
4.738-5.0630.305110.2062110.212220.8850.9371000.195
5.063-5.4660.241110.2382020.2382130.8660.9271000.215
5.466-5.9830.34590.2261830.2311920.8830.9261000.214
5.983-6.6820.324140.2271600.2341750.880.91699.42860.216
6.682-7.7010.43270.2231440.2311510.9090.931000.21
7.701-9.3960.18390.1641150.1651240.9570.9631000.162
9.396-13.14200.1821060.1821060.9741000.183
13.142-62.7930.48510.306600.307620.94198.38710.315

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