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- PDB-5suw: Crystal Structure of ToxT from Vibrio Cholerae O395 bound to 3-(8... -

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Basic information

Entry
Database: PDB / ID: 5suw
TitleCrystal Structure of ToxT from Vibrio Cholerae O395 bound to 3-(8-Methyl-1,2,3,4-tetrahydronaphthalen-1-yl)propanoic acid
ComponentsTCP pilus virulence regulatory protein
KeywordsTRANSCRIPTION REGULATOR / transcriptional activator / protein-inhibitor complex
Function / homology
Function and homology information


DNA-binding transcription activator activity / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / cytoplasm
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
Chem-70G / TCP pilus virulence regulatory protein
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKull, F.J. / Kelley, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072661 United States
CitationJournal: To Be Published
Title: Crystal Structure of ToxT from Vibrio Cholerae O395 bound to 3-(8-Methyl-1,2,3,4-tetrahydronaphthalen-1-yl)propanoic acid
Authors: Kull, F.J. / Kelley, A.R.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TCP pilus virulence regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7014
Polymers32,0921
Non-polymers6093
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.310, 81.110, 83.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TCP pilus virulence regulatory protein


Mass: 32092.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: tcpN, toxT, VC0395_A0363, VC395_0854 / Production host: Escherichia coli (E. coli) / References: UniProt: A5F384
#2: Chemical ChemComp-70G / 3-[(1R)-8-methyl-1,2,3,4-tetrahydronaphthalen-1-yl]propanoic acid


Mass: 218.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50% protein buffer: 20 mM Tris, 1 mM EDTA, 320 mM NaCl, pH 7.5 50% reservoir solution: 0.1 M MES pH 6.5 and 15% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2016
RadiationMonochromator: Si(111) double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→41.93 Å / Num. obs: 12783 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 11.35

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBG

3gbg


Resolution: 2.3→41.925 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.04
RfactorNum. reflection% reflection
Rfree0.2301 1181 5 %
Rwork0.1685 --
obs0.1717 23614 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 40 67 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072286
X-RAY DIFFRACTIONf_angle_d0.8543073
X-RAY DIFFRACTIONf_dihedral_angle_d15.5361371
X-RAY DIFFRACTIONf_chiral_restr0.052342
X-RAY DIFFRACTIONf_plane_restr0.004374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.40460.28451390.2412838X-RAY DIFFRACTION100
2.4046-2.53130.28821550.22812818X-RAY DIFFRACTION100
2.5313-2.68990.31311400.21442792X-RAY DIFFRACTION100
2.6899-2.89760.28461520.20162802X-RAY DIFFRACTION100
2.8976-3.18910.23121410.18752769X-RAY DIFFRACTION100
3.1891-3.65030.20761500.16352834X-RAY DIFFRACTION100
3.6503-4.59810.24691560.13152777X-RAY DIFFRACTION100
4.5981-41.93190.16981480.14552803X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.9046 Å / Origin y: -14.2444 Å / Origin z: -21.037 Å
111213212223313233
T0.2308 Å2-0.0104 Å20.0016 Å2-0.2618 Å2-0.0017 Å2--0.2978 Å2
L0.8405 °20.0789 °2-0.0063 °2-1.2317 °2-0.1654 °2--3.0111 °2
S0.0121 Å °0.0578 Å °-0.0556 Å °-0.1245 Å °-0.0299 Å °0.0927 Å °0.084 Å °-0.0805 Å °0.0234 Å °
Refinement TLS groupSelection details: all

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