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- PDB-7amt: Structure of LuxR with DNA (activation) -

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Basic information

Entry
Database: PDB / ID: 7amt
TitleStructure of LuxR with DNA (activation)
Components
  • DNA (5'-D(P*AP*TP*AP*AP*TP*GP*AP*CP*AP*TP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*AP*AP*TP*GP*TP*CP*AP*TP*TP*AP*T)-3')
  • HTH-type transcriptional regulator LuxR
KeywordsTRANSCRIPTION / transcription factor / DNA
Function / homologyTetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / DNA / DNA (> 10) / LuxR family transcriptional regulator
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, B. / Reverter, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098423-B-I00 Spain
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression.
Authors: Zhang, J. / Liu, B. / Gu, D. / Hao, Y. / Chen, M. / Ma, Y. / Zhou, X. / Reverter, D. / Zhang, Y. / Wang, Q.
History
DepositionOct 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: HTH-type transcriptional regulator LuxR
A: HTH-type transcriptional regulator LuxR
E: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*AP*AP*TP*GP*TP*CP*AP*TP*TP*AP*T)-3')
F: DNA (5'-D(P*AP*TP*AP*AP*TP*GP*AP*CP*AP*TP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)63,4894
Polymers63,4894
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-57 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.906, 68.906, 123.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein HTH-type transcriptional regulator LuxR / LuxR family transcriptional regulator / Quorum sensing regulator LuxR / Quorum-sensing II master ...LuxR family transcriptional regulator / Quorum sensing regulator LuxR / Quorum-sensing II master regulator / TetR/AcrR family transcriptional regulator


Mass: 25304.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria)
Gene: valR, luxR, AL539_16930, AOG25_16695, AT730_08150, K06K5_26160
Production host: Escherichia coli (E. coli) / References: UniProt: B4X9Q4
#2: DNA chain DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*AP*AP*TP*GP*TP*CP*AP*TP*TP*AP*T)-3')


Mass: 6435.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio alginolyticus (bacteria)
#3: DNA chain DNA (5'-D(P*AP*TP*AP*AP*TP*GP*AP*CP*AP*TP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*A)-3')


Mass: 6444.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio alginolyticus (bacteria)

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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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 50mM Sodium Formate, 50mM Tris PH7.5, 22% PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9191 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 2.543→61.966 Å / Num. obs: 18962 / % possible obs: 99.8 % / Redundancy: 13.7 % / CC1/2: 0.984 / Net I/σ(I): 11.3
Reflection shellResolution: 2.543→2.552 Å / Num. unique obs: 156 / CC1/2: 0.581

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AMN

7amn


Resolution: 2.6→60.223 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 849 4.79 %
Rwork0.2202 16893 -
obs0.2216 17742 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.81 Å2 / Biso mean: 105.22 Å2 / Biso min: 44.05 Å2
Refinement stepCycle: final / Resolution: 2.6→60.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 861 0 0 3850
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044013
X-RAY DIFFRACTIONf_angle_d0.7925612
X-RAY DIFFRACTIONf_chiral_restr0.032635
X-RAY DIFFRACTIONf_plane_restr0.002575
X-RAY DIFFRACTIONf_dihedral_angle_d22.1281509
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.76290.31831140.31122874100
2.7629-2.97620.3611450.29082790100
2.9762-3.27570.29581480.2531276199
3.2757-3.74970.26631380.2244281499
3.7497-4.72390.26431670.21852790100
4.7239-60.220.20561370.19742864100
Refinement TLS params.Method: refined / Origin x: 32.1786 Å / Origin y: 22.4479 Å / Origin z: 7.8885 Å
111213212223313233
T0.5635 Å2-0.0471 Å2-0.032 Å2-0.5336 Å2-0.0146 Å2--0.3359 Å2
L3.0686 °2-0.9543 °2-0.1611 °2-7.4165 °2-0.1656 °2--2.3713 °2
S-0.0171 Å °-0.1245 Å °-0.1684 Å °-0.3 Å °-0.0802 Å °-0.2686 Å °0.3437 Å °-0.4365 Å °0.1174 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB12 - 199
2X-RAY DIFFRACTION1allA10 - 198
3X-RAY DIFFRACTION1allE1 - 21
4X-RAY DIFFRACTION1allF1 - 21

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