+Open data
-Basic information
Entry | Database: PDB / ID: 6a59 | ||||||
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Title | Structure of histone demethylase REF6 at 1.8A | ||||||
Components | Lysine-specific demethylase REF6 | ||||||
Keywords | DNA BINDING PROTEIN / Complex / histone demethylase REF6 / DNA / zinc finger | ||||||
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 / : / 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 / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Tian, Z. / Chen, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2020 Title: Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms. Authors: Tian, Z. / Li, X. / Li, M. / Wu, W. / Zhang, M. / Tang, C. / Li, Z. / Liu, Y. / Chen, Z. / Yang, M. / Ma, L. / Caba, C. / Tong, Y. / Lam, H.M. / Dai, S. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a59.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a59.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 6a59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/6a59 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/6a59 | HTTPS FTP |
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-Related structure data
Related structure data | 6a57C 6a58SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16521.723 Da / Num. of mol.: 1 / Fragment: Ig gamma-1 chain C region 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 | ||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 10, 2017 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 15648 / % possible obs: 99.7 % / Redundancy: 11.3 % / Rsym value: 0.089 / Net I/σ(I): 63.9 |
Reflection shell | Resolution: 1.82→1.85 Å / Num. unique obs: 755 / Rsym value: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A58 Resolution: 1.82→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.486 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.549 Å2
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Refinement step | Cycle: 1 / Resolution: 1.82→50 Å
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Refine LS restraints |
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