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- PDB-6qec: DNA binding domain of LUX ARRYTHMO in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6qec
TitleDNA binding domain of LUX ARRYTHMO in complex with DNA
Components
  • (DNA (5'-D(*AP*TP*TP*CP*GP*AP*AP*TP*AP*T*TP*AP*TP*AP*TP*TP*CP*GP*AP*A)-3')) x 2
  • Transcription factor LUX
KeywordsCIRCADIAN CLOCK PROTEIN / protein-DNA complex Myb domain
Function / homology
Function and homology information


positive regulation of circadian rhythm / circadian rhythm / regulation of circadian rhythm / transcription regulator complex / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Transcription factor LUX/BOA-like / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / Homeodomain-like / SANT/Myb domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Transcription factor LUX
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZubieta, C. / Nayak, A.
Funding support France, 1items
OrganizationGrant numberCountry
ATIP-Avenir France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular mechanisms of Evening Complex activity inArabidopsis.
Authors: Silva, C.S. / Nayak, A. / Lai, X. / Hutin, S. / Hugouvieux, V. / Jung, J.H. / Lopez-Vidriero, I. / Franco-Zorrilla, J.M. / Panigrahi, K.C.S. / Nanao, M.H. / Wigge, P.A. / Zubieta, C.
History
DepositionJan 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
U: DNA (5'-D(*AP*TP*TP*CP*GP*AP*AP*TP*AP*T*TP*AP*TP*AP*TP*TP*CP*GP*AP*A)-3')
B: DNA (5'-D(*AP*TP*TP*CP*GP*AP*AP*TP*AP*T*TP*AP*TP*AP*TP*TP*CP*GP*AP*A)-3')
A: Transcription factor LUX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8635
Polymers13,6793
Non-polymers1842
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-8 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.758, 51.795, 35.993
Angle α, β, γ (deg.)90.000, 110.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*AP*TP*TP*CP*GP*AP*AP*TP*AP*T*TP*AP*TP*AP*TP*TP*CP*GP*AP*A)-3')


Mass: 3043.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#2: DNA chain DNA (5'-D(*AP*TP*TP*CP*GP*AP*AP*TP*AP*T*TP*AP*TP*AP*TP*TP*CP*GP*AP*A)-3')


Mass: 3043.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: Protein Transcription factor LUX / Protein LUX ARRHYTHMO / Protein PHYTOCLOCK 1


Mass: 7593.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LUX, PCL1, At3g46640, F12A12.160 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SNB4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M BisTris Propane, pH 6.5, 20% PEG 3350 and 0.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.66→30.673 Å / Num. obs: 12519 / % possible obs: 93.5 % / Redundancy: 2.55 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.053 / Χ2: 1.061 / Net I/σ(I): 9.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.66-1.711.9350.5551.27900.8120.73479.2
1.71-1.752.4170.5451.618730.8540.68993.4
1.75-1.82.6220.4851.999240.8830.60597.3
1.8-1.862.6510.3652.498700.9310.45297.1
1.86-1.922.5880.2743.128610.9460.34197
1.92-1.992.4940.23.888080.9680.25195.7
1.99-2.062.5670.1764.727920.9760.21997.1
2.06-2.152.6660.1326.187570.9860.16396.4
2.15-2.242.610.1157.187380.9880.14396.9
2.24-2.352.5570.088.686970.9940.09995.2
2.35-2.482.4410.079.736420.9950.08693.4
2.48-2.632.6770.06411.846310.9950.07996.2
2.63-2.812.6670.05114.675710.9950.06393.3
2.81-3.032.5750.04716.795370.9960.05892
3.03-3.322.5820.04120.314590.9970.0586.3
3.32-3.722.7430.0424.274430.9950.04993.5
3.72-4.292.6730.03325.993910.9960.04192
4.29-5.262.560.03225.773320.9970.0490.7
5.26-7.432.7730.02926.842600.9970.03692.5
7.43-30.6732.6220.02127.551430.9990.02687.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LXU

5lxu


Resolution: 1.9→30.673 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.48
Details: anisotropy diffraction limit applied Tickle, I.J., Flensburg, C., Keller, P., Paciorek, W., Sharff, A., Vonrhein, C., Bricogne, G. (2018). STARANISO (http://staraniso.globalphasing.org/cgi- ...Details: anisotropy diffraction limit applied Tickle, I.J., Flensburg, C., Keller, P., Paciorek, W., Sharff, A., Vonrhein, C., Bricogne, G. (2018). STARANISO (http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). Cambridge, United Kingdom: Global Phasing Ltd.
RfactorNum. reflection% reflection
Rfree0.2392 363 4.8 %
Rwork0.1919 --
obs0.1942 7556 84.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.84 Å2 / Biso mean: 24.9614 Å2 / Biso min: 9.31 Å2
Refinement stepCycle: final / Resolution: 1.9→30.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 403 28 137 1102
Biso mean--43.68 29.8 -
Num. residues----85
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081011
X-RAY DIFFRACTIONf_angle_d1.0091444
X-RAY DIFFRACTIONf_chiral_restr0.05162
X-RAY DIFFRACTIONf_plane_restr0.006112
X-RAY DIFFRACTIONf_dihedral_angle_d22.97538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-2.1750.3322930.24921964205769
2.175-2.740.27381400.23582596273692
2.74-30.6770.20481300.16112633276391

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