+Open data
-Basic information
Entry | Database: PDB / ID: 6j0d | ||||||
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Title | Crystal structure of OsSUF4 | ||||||
Components | transcription factor | ||||||
Keywords | TRANSCRIPTION / transcription factor | ||||||
Function / homology | Function and homology information regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wang, B. / Luo, Q. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: The transcription factor OsSUF4 interacts with SDG725 in promoting H3K36me3 establishment. Authors: Liu, B. / Liu, Y. / Wang, B. / Luo, Q. / Shi, J. / Gan, J. / Shen, W.H. / Yu, Y. / Dong, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j0d.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j0d.ent.gz | 20.5 KB | Display | PDB format |
PDBx/mmJSON format | 6j0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0d ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 11171.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q653D5 | ||
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#2: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Hepes pH7.0,PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→52.34 Å / Num. obs: 8598 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.9→1.97 Å / CC1/2: 0.831 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→52.34 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.802 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.133 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. 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: 24.294 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→52.34 Å
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Refine LS restraints |
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