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- PDB-5lxu: Structure of the DNA-binding domain of LUX ARRHYTHMO -

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Basic information

Entry
Database: PDB / ID: 5lxu
TitleStructure of the DNA-binding domain of LUX ARRHYTHMO
Components
  • (DNA (5'-D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')) x 2
  • Transcription factor LUX
KeywordsDNA BINDING PROTEIN / DNA-binding / transcription factor / MYB domain / three helix bundle
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 / SAD / Resolution: 2.14 Å
AuthorsZubieta, C. / Nanao, M.H.
Funding support France, 1items
OrganizationGrant numberCountry
ATIP-Avenir France
CitationJournal: To Be Published
Title: Structure of the DNA-binding domain of LUX ARRHYTHMO
Authors: Zubieta, C. / Silva, C.S. / Lai, X. / Wigge, P. / Nanao, M.H. / Nayak, A.
History
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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
A: Transcription factor LUX
U: DNA (5'-D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')
B: DNA (5'-D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)12,9033
Polymers12,9033
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-9 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.160, 32.830, 53.760
Angle α, β, γ (deg.)90.000, 98.610, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Transcription factor LUX / Protein LUX ARRHYTHMO / Protein PHYTOCLOCK 1


Mass: 6814.810 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
#2: DNA chain DNA (5'-D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')


Mass: 3035.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(*AP*TP*GP*CP*GP*TP*AP*TP*CP*TP*TP*AP*GP*AP*TP*AP*CP*GP*CP*A)-3')


Mass: 3053.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M bis-tris propane, 20% PEG 3350, 0.2M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.14→42 Å / Num. obs: 13640 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 1.47 % / Biso Wilson estimate: 57.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Net I/σ(I): 13.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
2.14-2.220.880.4521.590.65154.9
2.22-2.310.2822.590.82972.9
2.31-2.410.2113.70.91293.3
2.41-2.540.1395.110.96293.3
2.54-2.70.0977.160.97791.1
2.7-2.90.0639.880.99293.6
2.9-3.20.04214.440.99891.8
3.2-3.660.02821.080.99891.5
3.66-4.610.0229.140.99894.4
4.610.01932.790.99991.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHELXphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.14→41.68 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.248 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.232 379 5.01 %RANDOM
Rwork0.195 ---
obs0.197 7572 91.8 %-
Displacement parametersBiso max: 121.53 Å2 / Biso mean: 56.45 Å2 / Biso min: 34.83 Å2
Baniso -1Baniso -2Baniso -3
1--14.1243 Å20 Å2-2.9949 Å2
2--5.2588 Å20 Å2
3---8.8655 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.14→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms466 406 0 93 965
Biso mean---58.16 -
Num. residues----77
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d272SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes8HARMONIC2
X-RAY DIFFRACTIONt_gen_planes90HARMONIC5
X-RAY DIFFRACTIONt_it934HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion121SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1002SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d934HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1348HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion22.21
LS refinement shellResolution: 2.14→2.39 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.268 82 4.83 %
Rwork0.229 1617 -
all-1699 -
obs--74.07 %
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)
13.1346-0.0486-0.04363.6288-0.37824.4798-0.02140.11280.0962-0.04410.08090.0336-0.138-0.5334-0.0595-0.06920.06330.00520.02120.0004-0.1186-7.544731.034468.1326
25.1670.1069-0.33397.6549-1.85633.67210.08040.0151-0.0938-0.1244-0.229-0.56930.03470.26530.1486-0.0774-0.00120.0166-0.1401-0.0374-0.03136.557428.237665.5056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A144 - 200
2X-RAY DIFFRACTION2{ U|* }U1 - 29

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