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- PDB-6utc: Intra-chain disulfide bonded ToxR periplasmic domain from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 6utc
TitleIntra-chain disulfide bonded ToxR periplasmic domain from Vibrio vulnificus
ComponentsTranscriptional activator ToxR
KeywordsDNA BINDING PROTEIN / Sensor / Periplasm / ToxR / alpha-beta
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
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
Transcriptional regulator
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.249 Å
AuthorsMidgett, C.R. / Swindell, R.A. / Kull, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI140740 United States
CitationJournal: Sci Rep / Year: 2020
Title: A disulfide constrains the ToxR periplasmic domain structure, altering its interactions with ToxS and bile-salts.
Authors: Midgett, C.R. / Swindell, R.A. / Pellegrini, M. / Jon Kull, F.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: 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
A: Transcriptional activator ToxR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7452
Polymers11,6491
Non-polymers961
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.970, 40.440, 50.280
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 Transcriptional activator ToxR / Transcriptional regulator / Transmembrane transcription activator


Mass: 11649.110 Da / Num. of mol.: 1 / Fragment: periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: toxR, CRN46_04050, D8T65_08455, FORC36_0761 / Plasmid: pET-VvToxRp / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express / References: UniProt: Q9RP86
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.74 Å3/Da / Density % sol: 29.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 4 mg/ml VvToxRp, 2.0 M Ammonium Sulfate, 0.1 M Na Cacodylate pH 6.3
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.249→28.43 Å / Num. obs: 20411 / % possible obs: 87.8 % / Redundancy: 11.2 % / CC1/2: 1 / Net I/σ(I): 23.84
Reflection shellResolution: 1.249→1.294 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.9187 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1084 / CC1/2: 0.474 / Rpim(I) all: 0.4217 / Rrim(I) all: 1.018 / % possible all: 47.13

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-Met-VvToxRp

Resolution: 1.249→28.428 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.81
RfactorNum. reflection% reflection
Rfree0.2126 3748 9.83 %
Rwork0.1925 --
obs0.1944 20411 87.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.4 Å2 / Biso mean: 23.79 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 1.249→28.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 0 5 104 817
Biso mean--24.27 32.84 -
Num. residues----91
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2491-1.26490.452550.426563042
1.2649-1.28160.3966850.370164046
1.2816-1.29910.4264790.341476852
1.2991-1.31770.4197960.337882858
1.3177-1.33730.3366910.329890061
1.3373-1.35820.27031160.334899268
1.3582-1.38050.28111170.2913109676
1.3805-1.40430.33941400.2847122284
1.4043-1.42980.29211530.2592137493
1.4298-1.45730.25621500.2254137196
1.4573-1.48710.28911600.2175142897
1.4871-1.51940.21181470.2061141598
1.5194-1.55480.21541680.2136139997
1.5548-1.59360.24691600.21091454100
1.5936-1.63670.22981550.1965141898
1.6367-1.68490.23891560.2035148199
1.6849-1.73930.20691520.19661447100
1.7393-1.80140.19771580.2062143699
1.8014-1.87350.22261530.1937144799
1.8735-1.95880.22241550.1937146199
1.9588-2.0620.21351540.19681436100
2.062-2.19120.1921690.18661451100
2.1912-2.36030.1851580.1821464100
2.3603-2.59770.2471490.19081451100
2.5977-2.97320.20511570.18681462100
2.9732-3.74460.21061550.17621476100
3.7446-28.4280.16681600.16251451100

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