+Open data
-Basic information
Entry | Database: PDB / ID: 6qec | ||||||
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Title | DNA binding domain of LUX ARRYTHMO in complex with DNA | ||||||
Components |
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Keywords | CIRCADIAN CLOCK PROTEIN / protein-DNA complex Myb domain | ||||||
Function / homology | Function and homology information positive regulation of circadian rhythm / regulation of circadian rhythm / circadian rhythm / transcription regulator complex / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zubieta, C. / Nayak, A. | ||||||
Funding support | France, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qec.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qec.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 6qec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qec_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 6qec_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 6qec_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 6qec_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/6qec ftp://data.pdbj.org/pub/pdb/validation_reports/qe/6qec | HTTPS FTP |
-Related structure data
Related structure data | 5lxuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3043.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) | ||
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#2: DNA chain | Mass: 3043.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) | ||
#3: Protein | 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 | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.84 Å2 / Biso mean: 24.9614 Å2 / Biso min: 9.31 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→30.673 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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