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Yorodumi- PDB-6ip4: Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ip4 | ||||||
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Title | Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with NOG and an H3K27me3 peptide | ||||||
Components |
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Keywords | GENE REGULATION / histone modification / flowering / epigenetics | ||||||
Function / homology | Function and homology information negative regulation of short-day photoperiodism, flowering / long-day photoperiodism / negative regulation of long-day photoperiodism, flowering / histone H3K27me2/H3K27me3 demethylase activity / flower development / chromocenter / 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 / plastid / response to temperature stimulus ...negative regulation of short-day photoperiodism, flowering / long-day photoperiodism / negative regulation of long-day photoperiodism, flowering / histone H3K27me2/H3K27me3 demethylase activity / flower development / chromocenter / 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 / plastid / response to temperature stimulus / negative regulation of gene expression, epigenetic / histone demethylase activity / structural constituent of chromatin / nucleosome / histone binding / chromatin remodeling / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hu, H. / Du, J. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor. Authors: Zheng, S. / Hu, H. / Ren, H. / Yang, Z. / Qiu, Q. / Qi, W. / Liu, X. / Chen, X. / Cui, X. / Li, S. / Zhou, B. / Sun, D. / Cao, X. / Du, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ip4.cif.gz | 214.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ip4.ent.gz | 171.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ip4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ip4_validation.pdf.gz | 482.7 KB | Display | wwPDB validaton report |
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Full document | 6ip4_full_validation.pdf.gz | 500.9 KB | Display | |
Data in XML | 6ip4_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 6ip4_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ip4 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ip4 | HTTPS FTP |
-Related structure data
Related structure data | 6ip0SC 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 on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 55335.070 Da / Num. of mol.: 1 / Fragment: UNP residues 90-578 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: F4KIX0 |
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#2: Protein/peptide | Mass: 1129.311 Da / Num. of mol.: 1 / Fragment: UNP residues 25-36 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226 |
-Non-polymers , 5 types, 68 molecules
#3: Chemical | ChemComp-NI / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-OGA / | #6: Chemical | ChemComp-SO4 / #7: 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: 4.89 Å3/Da / Density % sol: 74.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M MES, pH 6.5, 8% dioxane, and 1.6M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 33189 / % possible obs: 93.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.091 / Net I/σ(I): 20.93 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 3316 / CC1/2: 0.615 / Rrim(I) all: 0.953 / Rsym value: 0.868 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IP0 Resolution: 2.6→49.367 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→49.367 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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