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- PDB-7amn: Structure of LuxR with DNA (repression) -

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Basic information

Entry
Database: PDB / ID: 7amn
TitleStructure of LuxR with DNA (repression)
Components
  • DNA (5'-D(P*TP*AP*TP*TP*GP*AP*TP*AP*AP*AP*AP*TP*TP*AP*TP*CP*AP*AP*TP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*AP*TP*TP*GP*AP*TP*AP*AP*TP*TP*TP*TP*AP*TP*CP*AP*AP*TP*A)-3')
  • HTH-type transcriptional regulator LuxR
KeywordsTRANSCRIPTION / transcription factor / DNA
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracyclin 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Quorum sensing regulator LuxR
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: HTH-type transcriptional regulator LuxR
A: HTH-type transcriptional regulator LuxR
E: DNA (5'-D(P*TP*AP*TP*TP*GP*AP*TP*AP*AP*AP*AP*TP*TP*AP*TP*CP*AP*AP*TP*AP*A)-3')
F: DNA (5'-D(P*TP*TP*AP*TP*TP*GP*AP*TP*AP*AP*TP*TP*TP*TP*AP*TP*CP*AP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)63,4874
Polymers63,4874
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-53 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.339, 69.339, 123.206
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*TP*GP*AP*TP*AP*AP*AP*AP*TP*TP*AP*TP*CP*AP*AP*TP*AP*A)-3')


Mass: 6452.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio alginolyticus (bacteria)
#3: DNA chain DNA (5'-D(P*TP*TP*AP*TP*TP*GP*AP*TP*AP*AP*TP*TP*TP*TP*AP*TP*CP*AP*AP*TP*A)-3')


Mass: 6425.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio alginolyticus (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.27 %
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: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.236→61.603 Å / Num. obs: 28010 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.99 / Net I/σ(I): 15.3
Reflection shellResolution: 2.236→2.244 Å / Num. unique obs: 280 / CC1/2: 0.46

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.03 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 1259 4.89 %
Rwork0.2099 24464 -
obs0.2115 25723 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.71 Å2 / Biso mean: 83.57 Å2 / Biso min: 35.49 Å2
Refinement stepCycle: final / Resolution: 2.3→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3044 861 0 23 3928
Biso mean---80.09 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054069
X-RAY DIFFRACTIONf_angle_d0.8225686
X-RAY DIFFRACTIONf_chiral_restr0.033643
X-RAY DIFFRACTIONf_plane_restr0.003584
X-RAY DIFFRACTIONf_dihedral_angle_d21.5181536
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.39210.3421280.30272751100
2.3921-2.5010.31171550.27842676100
2.501-2.63280.30041320.26432728100
2.6328-2.79780.33251480.27842714100
2.7978-3.01380.29021370.26742736100
3.0138-3.3170.27431090.2416270298
3.317-3.79680.24511790.2104267599
3.7968-4.7830.23441400.19142717100
4.783-49.030.19321310.1709276599
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)
15.91291.7752-0.08186.39460.35822.6737-0.29990.60520.7688-0.55030.24151.1857-0.3434-0.66930.05520.6640.0989-0.10390.55270.04810.5724-9.16924.3673-4.4487
25.1277-0.60531.52294.0833-0.75033.4408-0.22270.0283-0.2525-0.15260.29360.52780.03-0.851-0.05120.5049-0.07690.04680.5476-0.05580.3676-9.91451.1028-3.0093
32.006-0.17870.7079.4839-0.9011.99320.0779-0.0934-0.10750.9917-0.4651-2.4377-0.11750.19840.3120.5684-0.062-0.16620.4314-0.06361.230521.469911.54318.2877
42.19251.63650.63592.1442-0.85871.46030.1993-0.0715-0.03620.1534-0.6802-2.3758-0.24780.14860.41070.74890.0403-0.1540.4401-0.00221.117121.439710.60288.4096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq -10:9999)A-10 - 9999
2X-RAY DIFFRACTION2(chain B and resseq -10:9999)B-10 - 9999
3X-RAY DIFFRACTION3(chain E and resseq -10:9999)E-10 - 9999
4X-RAY DIFFRACTION4(chain F and resseq -10:9999)F-10 - 9999

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