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Yorodumi- PDB-7wq5: Crystal structure of Arabidopsis transcriptional factor WRINKLED1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wq5 | ||||||
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Title | Crystal structure of Arabidopsis transcriptional factor WRINKLED1 with dsDNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / transcriptional factor | ||||||
Function / homology | Function and homology information positive regulation of cutin biosynthetic process / triglyceride biosynthetic process / regulation of carbohydrate metabolic process / ethylene-activated signaling pathway / response to sucrose / regulation of glycolytic process / lipid biosynthetic process / lipid metabolic process / kinase binding / DNA-binding transcription factor activity ...positive regulation of cutin biosynthetic process / triglyceride biosynthetic process / regulation of carbohydrate metabolic process / ethylene-activated signaling pathway / response to sucrose / regulation of glycolytic process / lipid biosynthetic process / lipid metabolic process / kinase binding / DNA-binding transcription factor activity / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Zhu, Q. / Gao, Y.G. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Molecular basis of the key regulator WRINKLED1 in plant oil biosynthesis. Authors: Qiao, Z. / Kong, Q. / Tee, W.T. / Lim, A.R.Q. / Teo, M.X. / Olieric, V. / Low, P.M. / Yang, Y. / Qian, G. / Ma, W. / Gao, Y.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wq5.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wq5.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 7wq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/7wq5 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/7wq5 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 29202.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRI1, ASML1, At3g54320, T12E18.10, T12E18.20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6X5Y6 #2: DNA chain | Mass: 7516.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) #3: DNA chain | Mass: 7222.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) #4: Chemical | ChemComp-NH4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.16 Å3/Da / Density % sol: 43.11 % |
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Crystal grow | Temperature: 293.15 K / Method: evaporation / Details: PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40 Å / Num. obs: 32013 / % possible obs: 99.46 % / Redundancy: 26 % / Biso Wilson estimate: 71.98 Å2 / CC1/2: 1 / Rrim(I) all: 0.067 / Net I/σ(I): 32.27 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 26 % / Mean I/σ(I) obs: 1.47 / Num. unique obs: 3176 / CC1/2: 0.708 / Rrim(I) all: 2.85 / % possible all: 99.81 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→39.75 Å / SU ML: 0.4635 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.4836 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 81.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→39.75 Å
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Refine LS restraints |
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LS refinement shell |
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