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- PDB-5sux: Crystal Structure of ToxT from Vibrio Cholerae O395 bound to (E)-... -

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Basic information

Entry
Database: PDB / ID: 5sux
TitleCrystal Structure of ToxT from Vibrio Cholerae O395 bound to (E)-4-(8-methylnaphthalen-1-yl)but-3-enoic acid
ComponentsAraC family transcriptional regulator
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / transcriptional activator / protein-inhibitor complex / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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 / 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 / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. ...ToxT, HTH1 motif / Jelly Rolls - #810 / ToxT, HTH1 motif superfamily / 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 / Helix-turn-helix domain / 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
(3E)-4-(8-methylnaphthalen-1-yl)but-3-enoic acid / Pilus/toxin transcriptional regulator ToxT
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 (E)-4-(8-methylnaphthalen-1-yl)but-3-enoic 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 1.4Mar 6, 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: AraC family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7094
Polymers32,0921
Non-polymers6173
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.520, 80.960, 84.490
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 AraC family transcriptional regulator / 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 (bacteria)
Gene: toxT, tcpN, EN12_04130, ERS013198_02000, ERS013199_00625, ERS013200_01425, ERS013202_00629, ERS013206_00617, ERS013207_01424
Production host: Escherichia coli (E. coli) / References: UniProt: Q7BGC0
#2: Chemical ChemComp-70H / (3E)-4-(8-methylnaphthalen-1-yl)but-3-enoic acid


Mass: 226.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 43.03 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→42.25 Å / Num. obs: 2564 / % possible obs: 99.8 % / Redundancy: 4.1 % / Net I/σ(I): 11.91

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.245 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.06
RfactorNum. reflection% reflection
Rfree0.2296 1835 5.09 %
Rwork0.1886 --
obs0.1907 36076 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→42.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 41 79 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032274
X-RAY DIFFRACTIONf_angle_d0.6113058
X-RAY DIFFRACTIONf_dihedral_angle_d15.0721358
X-RAY DIFFRACTIONf_chiral_restr0.044340
X-RAY DIFFRACTIONf_plane_restr0.002373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05420.3511320.32892621X-RAY DIFFRACTION100
2.0542-2.11470.35631550.27912614X-RAY DIFFRACTION100
2.1147-2.18290.29731320.26012634X-RAY DIFFRACTION100
2.1829-2.26090.27231470.2352685X-RAY DIFFRACTION100
2.2609-2.35140.26361480.2232644X-RAY DIFFRACTION100
2.3514-2.45840.23241240.20942653X-RAY DIFFRACTION100
2.4584-2.5880.26071520.20692636X-RAY DIFFRACTION100
2.588-2.75020.23051490.19052630X-RAY DIFFRACTION100
2.7502-2.96250.26751370.19182645X-RAY DIFFRACTION100
2.9625-3.26050.23641440.18182630X-RAY DIFFRACTION99
3.2605-3.7320.23471280.16732626X-RAY DIFFRACTION99
3.732-4.7010.17591480.14542595X-RAY DIFFRACTION98
4.701-42.25440.19171390.1712628X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.8967 Å / Origin y: -14.258 Å / Origin z: -21.2521 Å
111213212223313233
T0.147 Å2-0.0018 Å20.0027 Å2-0.1534 Å2-0.0019 Å2--0.1657 Å2
L0.4494 °20.1997 °2-0.063 °2-0.7047 °2-0.2549 °2--0.9235 °2
S-0.0177 Å °0.0395 Å °-0.0514 Å °-0.0775 Å °0.0043 Å °0.0262 Å °0.0762 Å °-0.0326 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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