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Open data
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Basic information
Entry | Database: PDB / ID: 6jnm | ||||||
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Title | REF6 ZnF2-4-NAC004-mC3 complex | ||||||
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![]() | DNA BINDING PROTEIN/DNA / REF6 / zinc finger / 5mC / DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() 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 / response to brassinosteroid / sugar mediated signaling pathway / unidimensional cell growth ...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 / response to brassinosteroid / sugar mediated signaling pathway / 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 / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / 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 / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yao, Q.Q. / Wu, B.X. / Ma, J.B. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 60.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.8 KB | Display | ![]() |
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Full document | ![]() | 468.5 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jnlSC ![]() 6jnnC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12026.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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 #2: DNA chain | Mass: 3639.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 5CM / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3697.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16% PEG 3,350, 0.03 M citrate acid, 0.07 M Bis-Tris propane pH 7.6 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2017 |
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: 35297 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 4.241 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 1.02 / Num. unique obs: 3546 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JNL Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.905 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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