+Open data
-Basic information
Entry | Database: PDB / ID: 6j4f | ||||||
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Title | Crystal structure of the AtWRKY2 domain | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / WRKY transcription factors N-terminal WRKY domain / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information longitudinal axis specification / pollen development / establishment of cell polarity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Xu, Y.P. / Xu, H. / Wang, B. / Su, X.D. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the AtWRKY2 domain Authors: Xu, Y.P. / Xu, H. / Wang, B. / Su, X.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j4f.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j4f.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 6j4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j4f_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
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Full document | 6j4f_full_validation.pdf.gz | 469 KB | Display | |
Data in XML | 6j4f_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 6j4f_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/6j4f ftp://data.pdbj.org/pub/pdb/validation_reports/j4/6j4f | HTTPS FTP |
-Related structure data
Related structure data | 2aydS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9631.860 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY2, At5g56270, K24C1.9, MXK23.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FG77 #2: DNA chain | Mass: 4569.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) #3: DNA chain | Mass: 4609.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 3.53 Å3/Da / Density % sol: 65.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Lithium sulfate, 0.1M MES pH 6.0, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.58 Å / Num. obs: 17894 / % possible obs: 93.47 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Net I/σ(I): 9.59 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 1813 / CC1/2: 0.926 / Rpim(I) all: 0.29 / Rrim(I) all: 0.55 / % possible all: 96.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ayd Resolution: 2.4→29.58 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.58 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 54.5719 Å / Origin y: 1.9362 Å / Origin z: -27.3918 Å
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Refinement TLS group | Selection details: all |