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Yorodumi- PDB-4e8u: Crystal structure of Arabidopsis IDN2 XS domain along with a smal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e8u | ||||||
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Title | Crystal structure of Arabidopsis IDN2 XS domain along with a small segment of adjacent coiled-coil region | ||||||
Components | Putative uncharacterized protein T8P19.180 | ||||||
Keywords | RNA BINDING PROTEIN / XS domain / RNA directed DNA methylation / RNA | ||||||
Function / homology | Function and homology information heterochromatin formation => GO:0031507 / regulatory ncRNA-mediated gene silencing / : / regulation of double-strand break repair via homologous recombination / response to cadmium ion / RNA binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD (using a smaller construct), molecular replacement / Resolution: 2.701 Å | ||||||
Authors | Simanshu, D.K. / Patel, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Authors: Ausin, I. / Greenberg, M.V. / Simanshu, D.K. / Hale, C.J. / Vashisht, A.A. / Simon, S.A. / Lee, T.F. / Feng, S. / Espanola, S.D. / Meyers, B.C. / Wohlschlegel, J.A. / Patel, D.J. / Jacobsen, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e8u.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e8u.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 4e8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/4e8u ftp://data.pdbj.org/pub/pdb/validation_reports/e8/4e8u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.999664, -0.003911, -0.02561), Vector: |
-Components
#1: Protein | Mass: 19632.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IDN2, T8P19.180 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9SMN2, UniProt: Q8VZ79*PLUS #2: Chemical | ChemComp-SO4 / #3: 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: 4.13 Å3/Da / Density % sol: 70.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M BIS-TRIS pH 6.5, 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2010 Details: Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 18040 / % possible obs: 99 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.087 / Χ2: 2.453 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD (using a smaller construct), molecular replacement Resolution: 2.701→29.888 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.36 / Cross valid method: R-Free / σ(F): 0.1 / Phase error: 37.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.948 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.8 Å2 / Biso mean: 82.6751 Å2 / Biso min: 18.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.701→29.888 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 16.4628 Å / Origin y: 23.7646 Å / Origin z: 72.2328 Å
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Refinement TLS group |
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