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- PDB-6ide: Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex p... -

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Basic information

Entry
Database: PDB / ID: 6ide
TitleCrystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design
Components
  • DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*AP*AP*TP*CP*CP*CP*CP*CP*CP*T)-3')
  • DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*TP*TP*TP*CP*CP*CP*CP*CP*CP*T)-3')
  • Transcriptional regulator LuxR family
KeywordsTRANSCRIPTION/DNA / Vibrio cholera / Quorum sensing / transcription regulator / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
PAS fold-4 / PAS fold / 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 / DNA / DNA (> 10) / Transcriptional regulator LuxR family / Transcriptional regulator LuxR family
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsWu, H. / Li, M.J. / Guo, H.J. / Zhou, H. / Li, B. / Xu, Q. / Xu, C.Y. / Yu, F. / He, J.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570740 China
National Natural Science Foundation of China81330076 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Crystal structure of theVibrio choleraeVqmA-ligand-DNA complex provides insight into ligand-binding mechanisms relevant for drug design.
Authors: Wu, H. / Li, M. / Guo, H. / Zhou, H. / Li, B. / Xu, Q. / Xu, C. / Yu, F. / He, J.
History
DepositionSep 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator LuxR family
B: Transcriptional regulator LuxR family
C: DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*AP*AP*TP*CP*CP*CP*CP*CP*CP*T)-3')
D: DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*TP*TP*TP*CP*CP*CP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0206
Polymers68,7714
Non-polymers2482
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-94 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.780, 108.980, 214.320
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 Transcriptional regulator LuxR family


Mass: 28868.133 Da / Num. of mol.: 2 / Fragment: UNP residues 75-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6WEL7, UniProt: A0A655PXP1*PLUS
#2: DNA chain DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*AP*AP*TP*CP*CP*CP*CP*CP*CP*T)-3')


Mass: 5526.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#3: DNA chain DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*TP*TP*TP*CP*CP*CP*CP*CP*CP*T)-3')


Mass: 5508.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#4: Chemical ChemComp-A1U / 3,5-dimethylpyrazin-2-ol


Mass: 124.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.48 Å3/Da / Density % sol: 72.55 %
Crystal growTemperature: 301 K / Method: evaporation
Details: 3.85% polyethylene glycol (PEG) 3350 and 0.165 M K2HPO4/NaH2PO4 pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.51→53.58 Å / Num. obs: 43223 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Net I/σ(I): 18.9 / Num. measured all: 564429 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.51-2.5813.21.67531200.790.4751.74399.8
11.23-53.589.90.045660.9950.0140.04396.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.13_2998: ???refinement
Aimless0.6.2data scaling
CRANK2phasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.51→43.326 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.69
RfactorNum. reflection% reflection
Rfree0.2294 1997 4.63 %
Rwork0.1915 --
obs0.1932 43108 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.46 Å2 / Biso mean: 96.4558 Å2 / Biso min: 53.5 Å2
Refinement stepCycle: final / Resolution: 2.51→43.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 732 18 6 4331
Biso mean--69.14 69.95 -
Num. residues----490
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)
13.7627-0.80930.18522.0229-1.06231.55070.32350.8063-0.1302-0.444-0.1245-0.1514-0.11520.1537-0.10590.67320.0239-0.02070.8795-0.04840.73613.028628.19556.5193
22.64160.3288-0.00762.41170.93992.5851-0.04180.1112-0.0451-0.2728-0.0471-0.1833-0.18020.24940.11110.6362-0.00560.04360.7733-0.0060.737612.012128.900117.0418
31.50780.94790.8124.83181.39343.17980.0525-0.040.14420.5850.1597-0.03360.0443-0.3616-0.24520.82950.08590.06350.8942-0.02970.7546-2.502731.154241.602
41.9943-0.5906-0.28642.7818-0.77383.28250.0719-0.03470.0620.6368-0.020.2453-0.471-0.216-0.05750.79640.04930.02710.6705-0.06750.67590.19733.215641.5039
53.5036-0.32961.37071.3375-1.13742.6229-0.1179-0.1948-0.1401-0.21480.1010.09450.382-0.76170.0320.5973-0.07610.08020.8084-0.08640.6794-9.647423.611115.8805
62.0369-0.08440.32572.9225-1.02192.89120.05960.1001-0.33360.3389-0.0359-0.30710.35140.113-0.00720.97530.06020.06110.84340.04790.9314-0.855315.493342.0268
71.15990.0621-0.44070.93430.05990.17670.2012-0.17020.62260.90950.1201-0.593-0.1015-0.111-0.30092.0477-0.2149-0.05840.90990.09851.1261-5.91424.415859.2026
81.8431.0276-0.17615.26340.31412.4810.874-0.4808-0.10351.7903-1.2177-0.41550.4439-0.12680.21441.8763-0.0831-0.10091.1426-0.020.99610.862625.85263.5266
90.9461-1.16911.35284.49281.23584.7214-0.0597-0.13130.18640.9615-0.33820.90710.99110.82550.38442.18940.09270.04911.1457-0.13020.98843.005449.027263.5779
102.0403-0.09350.05421.41650.44391.70910.12160.0636-0.98841.46440.10490.3358-1.7372-0.2576-0.35411.68730.1557-0.0691.16360.00541.14856.733442.797459.1657
112.50881.82470.85513.53820.49832.13580.595-0.4771-0.13761.8757-0.8572-0.6016-0.2955-0.38190.21881.9664-0.1195-0.02661.05670.14851.02490.56321.010663.3849
120.41281.1136-1.23186.4398-0.74235.598-0.2065-0.9730.41181.4931-0.9097-1.8902-0.8813-0.21390.96912.0273-0.1889-0.22341.28050.2371.2753-2.4113-1.73263.3538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 33 )A2 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 120 )A34 - 120
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 180 )A121 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 238 )A181 - 238
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 135 )B2 - 135
6X-RAY DIFFRACTION6chain 'B' and (resid 136 through 236 )B136 - 236
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 5 )C1 - 5
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 15 )C6 - 15
9X-RAY DIFFRACTION9chain 'C' and (resid 16 through 18 )C16 - 18
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 5 )D1 - 5
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 15 )D6 - 15
12X-RAY DIFFRACTION12chain 'D' and (resid 16 through 18 )D16 - 18

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