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- PDB-6pb9: Crystal structure of unsaturated fatty acid bound ToxT K231A from... -

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Basic information

Entry
Database: PDB / ID: 6pb9
TitleCrystal structure of unsaturated fatty acid bound ToxT K231A from Vibrio cholerae strain SCE256
ComponentsToxin co-regulated pilus virulence regulatory protein
KeywordsDNA BINDING PROTEIN / AraC / XylS / virulence regulation / cholerae
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
ToxT, HTH1 motif / Jelly Rolls - #810 / ToxT, HTH1 motif superfamily / ToxT, N-terminal cupin-like domain / Bacterial regulatory helix-turn-helix proteins, AraC family / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. ...ToxT, HTH1 motif / Jelly Rolls - #810 / ToxT, HTH1 motif superfamily / ToxT, N-terminal cupin-like domain / Bacterial regulatory helix-turn-helix proteins, AraC family / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PALMITOLEIC ACID / Toxin co-regulated pilus virulence regulatory protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.109 Å
AuthorsCruite, J.T. / Kull, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI120068 United States
CitationJournal: Commun Biol / Year: 2019
Title: Structural basis for virulence regulation inVibrio choleraeby unsaturated fatty acid components of bile.
Authors: Cruite, J.T. / Kovacikova, G. / Clark, K.A. / Woodbrey, A.K. / Skorupski, K. / Kull, F.J.
History
DepositionJun 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin co-regulated pilus virulence regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4182
Polymers32,1631
Non-polymers2541
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.298, 46.858, 74.379
Angle α, β, γ (deg.)90.000, 98.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Toxin co-regulated pilus virulence regulatory protein


Mass: 32163.098 Da / Num. of mol.: 1 / Mutation: K231A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F5Q9
#2: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350

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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: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.109→28.21 Å / Num. obs: 15481 / % possible obs: 97.97 % / Redundancy: 6.7 % / Biso Wilson estimate: 43.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07214 / Rpim(I) all: 0.03006 / Rrim(I) all: 0.07827 / Net I/σ(I): 14.54
Reflection shellResolution: 2.109→2.185 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.6872 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 963 / CC1/2: 0.818 / Rpim(I) all: 0.2818 / Rrim(I) all: 0.7439 / % possible all: 92.81

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.109→28.21 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.29
RfactorNum. reflection% reflection
Rfree0.2803 1547 10 %
Rwork0.2292 --
obs0.2342 15473 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.28 Å2 / Biso mean: 53.5388 Å2 / Biso min: 21.26 Å2
Refinement stepCycle: final / Resolution: 2.109→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 18 34 2302
Biso mean--52.96 47.71 -
Num. residues----276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1087-2.17680.33291310.27071179131092
2.1768-2.25460.29011400.25611253139398
2.2546-2.34480.3151370.25911246138398
2.3448-2.45150.32361400.25741262140298
2.4515-2.58060.33871420.27491273141598
2.5806-2.74220.33931390.2711256139599
2.7422-2.95370.2871420.25231275141799
2.9537-3.25060.32931420.24771276141899
3.2506-3.72020.25921410.22351278141999
3.7202-4.68380.25691450.20351296144199
4.6838-28.9960.25091480.2091332148099

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