+Open data
-Basic information
Entry | Database: PDB / ID: 6jnl | ||||||
---|---|---|---|---|---|---|---|
Title | REF6 ZnF2-4-NAC004 complex | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN/DNA / REF6 / zinc finger / 5mC / DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information regulation of ethylene-activated signaling pathway / abscisic acid catabolic process / release of seed from dormancy / positive regulation of lateral root development / : / response to diterpene / : / heat acclimation / protein localization to heterochromatin / : ...regulation of ethylene-activated signaling pathway / abscisic acid catabolic process / release of seed from dormancy / positive regulation of lateral root development / : / response to diterpene / : / heat acclimation / protein localization to heterochromatin / : / sugar mediated signaling pathway / response to brassinosteroid / unidimensional cell growth / regulation of photoperiodism, flowering / systemic acquired resistance / vegetative to reproductive phase transition of meristem / : / ethylene-activated signaling pathway / histone H3K27me2/H3K27me3 demethylase activity / leaf development / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / response to abscisic acid / Ino80 complex / abscisic acid-activated signaling pathway / epigenetic regulation of gene expression / response to mechanical stimulus / protein homooligomerization / : / response to heat / sequence-specific DNA binding / positive regulation of gene expression / regulation of DNA-templated transcription / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Yao, Q.Q. / Wu, B.X. / Ma, J.B. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: DNA methylation repels targeting of Arabidopsis REF6. Authors: Qiu, Q. / Mei, H. / Deng, X. / He, K. / Wu, B. / Yao, Q. / Zhang, J. / Lu, F. / Ma, J. / Cao, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jnl.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jnl.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 6jnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/6jnl ftp://data.pdbj.org/pub/pdb/validation_reports/jn/6jnl | HTTPS FTP |
---|
-Related structure data
Related structure data | 6jnmC 6jnnC 4r2sS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 12026.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: REF6, JMJ12, PKDM9A, At3g48430, T29H11_50 / Production host: Escherichia coli (E. coli) References: UniProt: Q9STM3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
---|
-DNA chain , 2 types, 2 molecules DC
#2: DNA chain | Mass: 3625.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 3384.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 30 molecules
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-DA / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.55 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 3,350, 0.2 M NH4F |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 18924 / % possible obs: 99.9 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 52.16 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.59 / Num. unique obs: 1211 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R2S Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.888 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.583 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|