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- PDB-6kju: Huge conformation shift of Vibrio cholerae VqmA dimer in the abse... -

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Basic information

Entry
Database: PDB / ID: 6kju
TitleHuge conformation shift of Vibrio cholerae VqmA dimer in the absence of target DNA provides insight into DNA-binding mechanisms of LuxR-type receptors
ComponentsHelix-turn-helix transcriptional regulator
KeywordsTRANSCRIPTION / Vibrio cholera / Quorum sensing / transcription regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / 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-ol / Helix-turn-helix transcriptional regulator / Transcriptional regulator, LuxR family
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWu, H. / Li, M.J. / Guo, H.J. / Zhou, H. / Wang, W.W. / Xu, Q. / Xu, C.Y. / Yu, F. / He, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Large conformation shifts of Vibrio cholerae VqmA dimer in the absence of target DNA provide insight into DNA-binding mechanisms of LuxR-type receptors.
Authors: Wu, H. / Li, M. / Peng, C. / Yin, Y. / Guo, H. / Wang, W. / Xu, Q. / Zhou, H. / Xu, C. / Yu, F. / He, J.
History
DepositionJul 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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)57,5004
Polymers57,2522
Non-polymers2482
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-42 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.550, 84.510, 117.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 28625.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: C9J66_03310, EC575_07960, EN12_18880, ERS013215_03763, ET956_04375, EYB64_07770
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F0AZW0, UniProt: Q9KKM5*PLUS
#2: Chemical ChemComp-A1U / 3,5-dimethylpyrazin-2-ol


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.: 275 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18% polyethylene glycol (PEG) 3350, 0.2 M sodium citrate tribasic dihydrate pH 6.0 and 5% ethyl acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→34.92 Å / Num. obs: 51631 / % possible obs: 99.9 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.75-1.812.11.4883756199.8
7.83-34.929.80.052669198.8

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IDE

6ide


Resolution: 1.75→32.42 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.98
RfactorNum. reflection% reflection
Rfree0.1958 2512 4.87 %
Rwork0.1747 --
obs0.1757 51545 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.31 Å2 / Biso mean: 43.5174 Å2 / Biso min: 20.16 Å2
Refinement stepCycle: final / Resolution: 1.75→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 18 275 3839
Biso mean--27.73 45.55 -
Num. residues----448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.78370.35191380.33932679100
1.7837-1.82010.2951430.2955266599
1.8201-1.85970.25471350.2532701100
1.8597-1.90290.22881250.2099265399
1.9029-1.95050.24891580.2042666100
1.9505-2.00320.23861370.20362711100
2.0032-2.06220.21031400.19352682100
2.0622-2.12870.18751360.17612721100
2.1287-2.20480.20491430.17482697100
2.2048-2.2930.19931310.17792727100
2.293-2.39740.21191390.17442694100
2.3974-2.52370.23181270.18132744100
2.5237-2.68180.17671240.17972734100
2.6818-2.88870.21411390.18172738100
2.8887-3.17920.19831340.17472764100
3.1792-3.63870.16891630.16372748100
3.6387-4.58230.14991410.14352797100
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)
14.19370.2745-1.39091.4209-0.58952.73940.1154-0.18570.35940.0734-0.0815-0.0591-0.11010.0285-0.04290.24310.0133-0.00070.2389-0.05150.2757-22.065812.8979-7.002
27.13040.1057-1.81633.60991.48886.14250.00290.06380.509-0.1399-0.01940.0726-0.3692-0.04190.0210.20990.024-0.02410.22130.0160.285-33.95189.701-9.8365
36.30110.34762.80772.42791.33755.4010.0797-0.8182-0.4470.364-0.07360.02640.4889-0.3456-0.0470.27570.00970.03230.31830.07620.2614-30.7086-2.69840.7177
44.43610.23080.96292.74971.43624.3117-0.0017-0.2202-0.11960.13040.0682-0.06890.08310.2835-0.07980.18250.00220.02130.2220.02820.2445-24.6970.8345-5.7191
51.95260.40730.02323.6651-0.49591.7655-0.15870.2716-0.6513-0.0330.0564-0.23430.4822-0.11610.02660.44750.00150.12860.3235-0.06080.6107-22.918-19.6782-15.1326
69.14973.40321.73484.5466-0.27893.91820.0021-0.74460.04220.768-0.0921.02740.047-0.53530.07030.6946-0.03990.23360.43970.02140.7055-36.3476-17.5219-5.5713
71.7356-2.1232-0.08162.8359-0.46991.95260.0998-0.7762-0.72210.36650.22710.73270.5367-0.5354-0.2550.635-0.16620.13940.54020.12340.9116-34.1561-29.5719-7.487
85.73914.7799-2.67477.1354-4.22655.21230.3844-0.916-1.0851.0086-0.1421-0.51640.26550.29-0.16860.77140.02990.06210.46120.16060.9084-23.262-29.3148-1.5896
94.6724-1.1708-0.95453.18431.92333.40780.08910.1294-0.697-0.1551-0.0055-0.1350.40070.0848-0.11130.4648-0.00430.08050.2833-0.00290.5739-26.2524-17.1625-14.5364
103.51952.40735.67895.81963.11769.41550.117-0.4709-0.42680.57980.2119-0.56460.32280.5582-0.26130.39570.07180.0070.47030.01360.4086-19.683-7.2891-0.4023
113.0508-0.3061-0.11971.36410.36541.2521-0.0031-0.01070.11370.03740.0585-0.0404-0.03460.0501-0.08950.2085-0.00830.00520.1755-0.00770.2207-5.99547.8416-12.6163
124.3750.11760.03343.33511.77951.8777-0.16940.4465-0.51080.13690.15520.04490.24050.02960.0090.37940.00710.06010.3253-0.08170.362-5.8839-16.5692-23.4072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 33 )A5 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 58 )A34 - 58
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 77 )A59 - 77
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 120 )A78 - 120
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 168 )A121 - 168
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 183 )A169 - 183
7X-RAY DIFFRACTION7chain 'A' and (resid 184 through 198 )A184 - 198
8X-RAY DIFFRACTION8chain 'A' and (resid 199 through 212 )A199 - 212
9X-RAY DIFFRACTION9chain 'A' and (resid 213 through 227 )A213 - 227
10X-RAY DIFFRACTION10chain 'A' and (resid 228 through 239 )A228 - 239
11X-RAY DIFFRACTION11chain 'B' and (resid 4 through 131 )B4 - 131
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 239 )B132 - 239

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