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Yorodumi- PDB-7wsj: Crystal structure of the tandem B-box domain of Arabidopsis thali... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wsj | ||||||
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Title | Crystal structure of the tandem B-box domain of Arabidopsis thaliana CONSTANS | ||||||
Components | Zinc finger protein CONSTANS | ||||||
Keywords | PLANT PROTEIN / tandem b-box / Zn-coordinating motif / photoperiodic flowering | ||||||
Function / homology | Function and homology information far-red light signaling pathway / regulation of flower development / response to far red light / flower development / cell differentiation / DNA-binding transcription factor activity / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Dahal, P. / Pathak, D. / Kwon, E. / Kim, D.Y. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Crystal structure of a tandem B-box domain from Arabidopsis CONSTANS. Authors: Dahal, P. / Kwon, E. / Pathak, D. / Kim, D.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wsj.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wsj.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wsj_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7wsj_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7wsj_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 7wsj_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/7wsj ftp://data.pdbj.org/pub/pdb/validation_reports/ws/7wsj | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12012.432 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CO, At5g15840, F14F8_220 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q39057 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.91 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.5 Details: 1.39 M Lithium Sulfate, 4.55% MPD, 85 mM Imidazole-HCl pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1.28176 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28176 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.93 Å / Num. obs: 19958 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.584 / Num. unique obs: 2059 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→45.93 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.34 Å2 / Biso mean: 59.3381 Å2 / Biso min: 23.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→45.93 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 36.2184 Å / Origin y: 23.3896 Å / Origin z: 26.3455 Å
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Refinement TLS group |
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