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- PDB-6ugl: VqmA bound to DPO -

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Basic information

Entry
Database: PDB / ID: 6ugl
TitleVqmA bound to DPO
ComponentsHelix-turn-helix transcriptional regulator
KeywordsTRANSCRIPTION / Transcriptional activator protein of quorum sensing genes / 3 / 5-dimethylpyrazin-2-ol (DPO)
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
PAS fold-4 / PAS fold / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS domain / PAS domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
3,5-dimethylpyrazin-2(1H)-one / Helix-turn-helix transcriptional regulator
Similarity search - Component
Biological speciesVibrio cholerae O1 str. 2010EL-1786 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsPaczkowski, J.E. / Huang, X.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R37GM065859 United States
National Science Foundation (NSF, United States)MCB-1713731 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Mechanism underlying autoinducer recognition in theVibrio choleraeDPO-VqmA quorum-sensing pathway.
Authors: Huang, X. / Duddy, O.P. / Silpe, J.E. / Paczkowski, J.E. / Cong, J. / Henke, B.R. / Bassler, B.L.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
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: Helix-turn-helix transcriptional regulator
B: Helix-turn-helix transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3584
Polymers55,1092
Non-polymers2482
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-29 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.459, 84.680, 116.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Helix-turn-helix transcriptional regulator / LuxR family transcriptional regulator / PAS domain S-box protein / Transcriptional regulator / LuxR family


Mass: 27554.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 str. 2010EL-1786 (bacteria)
Gene: C9J66_03310, EC575_07960, EN12_18880, ERS013215_03763, EYB64_07770
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F0AZW0
#2: Chemical ChemComp-QOS / 3,5-dimethylpyrazin-2(1H)-one


Mass: 124.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N2O
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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M Tris pH 7.3, 16% PEG3350 and 0.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→28.9 Å / Num. obs: 32520 / % possible obs: 98.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 34.51 Å2 / Rrim(I) all: 0.158 / Net I/σ(I): 12.56
Reflection shellResolution: 2.03→2.1 Å / Num. unique obs: 2905 / Rrim(I) all: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→28.86 Å / SU ML: 0.3133 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.0948
RfactorNum. reflection% reflection
Rfree0.331 1990 6.12 %
Rwork0.2771 --
obs0.2803 32520 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.76 Å2
Refinement stepCycle: LAST / Resolution: 2.03→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 18 0 3225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743300
X-RAY DIFFRACTIONf_angle_d0.95484459
X-RAY DIFFRACTIONf_chiral_restr0.0532490
X-RAY DIFFRACTIONf_plane_restr0.0054562
X-RAY DIFFRACTIONf_dihedral_angle_d3.40291943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.44791210.38521854X-RAY DIFFRACTION86.06
2.08-2.140.4231400.34982169X-RAY DIFFRACTION99.35
2.14-2.20.40321420.32052164X-RAY DIFFRACTION99.14
2.2-2.270.39891410.31262165X-RAY DIFFRACTION99.7
2.27-2.350.41251420.31812163X-RAY DIFFRACTION99.48
2.35-2.440.381410.31262176X-RAY DIFFRACTION99.27
2.44-2.560.37331420.31892166X-RAY DIFFRACTION99.61
2.56-2.690.3541410.31052183X-RAY DIFFRACTION99.44
2.69-2.860.37911430.30092197X-RAY DIFFRACTION99.83
2.86-3.080.37951450.3072214X-RAY DIFFRACTION99.96
3.08-3.390.37481450.29162219X-RAY DIFFRACTION99.75
3.39-3.880.29771450.25632242X-RAY DIFFRACTION99.92
3.88-4.880.27341470.22122242X-RAY DIFFRACTION99.83
4.88-28.860.25811550.24982376X-RAY DIFFRACTION99.88

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