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- PDB-6ugl: Vibrio cholerae quorum-sensing receptor VqmA bound to its autoind... -

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Basic information

Entry
Database: PDB / ID: 6ugl
TitleVibrio cholerae quorum-sensing receptor VqmA bound to its autoinducer ligand 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 / Beta-Lactamase / PAS domain ...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 / Beta-Lactamase / PAS domain / PAS domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
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. / Jeffrey, P.D.
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
Revision 2.0Nov 19, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / cell / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_contact_author.id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.number_obs / _struct.title
Description: Model completeness
Details: Residues have been added, some conformations have been changed, waters have been added, and you'll notice that Rwork and Rfree are considerably lower. The S-S bond is real, and was missing ...Details: Residues have been added, some conformations have been changed, waters have been added, and you'll notice that Rwork and Rfree are considerably lower. The S-S bond is real, and was missing from the original model.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-39 kcal/mol
Surface area19260 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 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: 32521 / % 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
PHENIX1.17_3644refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→28.86 Å / SU ML: 0.2854 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.3787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2773 1990 6.12 %
Rwork0.2133 30531 -
obs0.2171 32521 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.13 Å2
Refinement stepCycle: LAST / Resolution: 2.03→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 18 165 3597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643511
X-RAY DIFFRACTIONf_angle_d0.76384751
X-RAY DIFFRACTIONf_chiral_restr0.0509529
X-RAY DIFFRACTIONf_plane_restr0.0085602
X-RAY DIFFRACTIONf_dihedral_angle_d17.54471265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.4161210.33771855X-RAY DIFFRACTION86.1
2.08-2.140.36871400.31052169X-RAY DIFFRACTION99.35
2.14-2.20.40971420.26842164X-RAY DIFFRACTION99.18
2.2-2.270.3211410.25732165X-RAY DIFFRACTION99.65
2.27-2.350.32781420.24062162X-RAY DIFFRACTION99.4
2.35-2.440.28311410.2432176X-RAY DIFFRACTION99.27
2.44-2.560.34071420.23712167X-RAY DIFFRACTION99.61
2.56-2.690.31621410.24062183X-RAY DIFFRACTION99.44
2.69-2.860.32481430.23422197X-RAY DIFFRACTION99.83
2.86-3.080.32711450.23132214X-RAY DIFFRACTION99.96
3.08-3.390.27841450.21932220X-RAY DIFFRACTION99.79
3.39-3.880.25881450.18722242X-RAY DIFFRACTION99.87
3.88-4.880.21411470.16282241X-RAY DIFFRACTION99.75
4.88-28.860.21981550.19772376X-RAY DIFFRACTION99.88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.64963309797-0.1033577295680.006514942379990.6147503574430.1696105922820.400065092138-0.003096834024860.0562167969299-0.4594088481210.0260462625660.01116791471050.01099155432020.0905959860349-0.0405698627229-0.006940829659960.222239602134-0.007249683861920.0004395888553110.2225935664210.005780832250690.46833803234231.425409346632.508149448445.3382232752
23.672359132310.516200093245-0.39955668753.95253343681-2.081332485423.0886690492-0.04968666720140.4675986494190.44227924356-0.03025952400170.0811964691193-0.0826857737252-0.1390729502190.0599226033432-0.03491302944520.3207998685750.012303984365-0.009092815260040.4105806029930.1851084442850.61658913074130.606765659458.404806596435.1845593386
38.017577687715.28865958015-5.467529641983.75528213005-3.620987698393.763136037760.0937804344786-0.467664667763-1.426824199410.0178579340257-0.4660419334610.4017267194770.3247026862360.5711130904370.3212242081220.2780398686430.02562594339170.001697270823520.3420968611460.03975850044730.69125901010941.111873758522.151013342947.8391252252
46.03404687212-0.283456472131.010223413541.14046667655-2.425707134946.042787630630.04031715336410.0940134235532-0.281009214403-0.198384107517-0.0666369656108-0.1021277933210.2745255866430.2303977803080.01464135868530.236046731978-0.00654372024632-0.0177403856840.204196153392-0.02454136810310.50182541488656.30447057433.230145693650.5458951189
51.978640485610.3168316520631.782772874882.9330969283-0.6008530368882.014571240560.144608074753-0.7289999434460.01056018694950.371284083553-0.167374669443-0.0324403682144-0.814977736220.351676974892-0.09519566645620.3464525913730.0243903672731-0.02441350335730.328757089165-0.1136868518440.51642120114556.357627920545.264599655458.8650254369
65.57510506242-0.311474523803-3.659704187991.07416434072-1.042517718117.185993043820.00162531650565-0.228888288462-0.0766468306316-0.0205789020050.0721724533349-0.00837103312282-0.054795365612-0.199379900584-0.1068552420250.208079136551-0.0122872844-0.01410289941960.2329894614310.01147634907710.45083657245150.146784453341.472100655252.7943405437
72.73148024207-0.2809813738350.3513884543016.443334738780.4642157318313.15113262566-0.008420863344020.3821786584720.765777251317-0.06461469014550.1462581921280.361026255506-0.536612441447-0.0842558637647-0.123836977250.4109934437970.0439819802759-0.02703623975430.3788202754430.05291077033360.79093006579748.605404134960.488153953743.6162914228
84.550675552475.52359408769-4.169652018636.95354127999-4.649144550034.422305222150.121700346494-0.285561522118-0.6329604196850.891904050913-0.384062255731-0.642949220415-1.109094629691.140298121520.2638676901540.553501377824-0.110445320939-0.04531258278530.482235242715-0.1473476649880.81554990567662.053064101359.917912750552.3455428814
93.94363604288-4.49424664050.4503340068925.22836568684-0.8739739280832.19503750443-0.4251922562880.05135172865041.348863522980.641432661480.290441774247-0.326588027381-1.057975696110.6767365223210.1397614480520.861505503361-0.349484886951-0.0421145018150.557709225324-0.06849628675141.0646715219160.7696952371.675380729850.120860598
107.987957355895.939270225225.835213653324.438059727314.352151183524.27243585842-0.260923451212-0.8034930857232.662544571731.17428756963-0.2885733666661.22172116519-0.738239479272-0.4093462393160.5309417165321.081556008890.1460020818050.1765362933940.522095014976-0.06424706296181.1269025181149.411035266372.280877490455.7308631172
110.654305457905-1.554634067731.767798972167.34752626924-3.631983466445.45040603218-0.05423743483420.1479786950051.103968502640.3188907607490.346863097748-0.0198550967157-0.41967378758-0.546383770898-0.3008795323450.2768058853240.0204050880572-0.02829503346720.3479598979810.01480190074460.65871562707549.786232681756.187646458948.610170303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 120 )
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 238 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 15 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 58 )
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 77 )
6X-RAY DIFFRACTION6chain 'B' and (resid 78 through 120 )
7X-RAY DIFFRACTION7chain 'B' and (resid 121 through 168 )
8X-RAY DIFFRACTION8chain 'B' and (resid 169 through 183 )
9X-RAY DIFFRACTION9chain 'B' and (resid 184 through 197 )
10X-RAY DIFFRACTION10chain 'B' and (resid 198 through 212 )
11X-RAY DIFFRACTION11chain 'B' and (resid 213 through 237 )

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