+Open data
-Basic information
Entry | Database: PDB / ID: 4quc | ||||||
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Title | Crystal structure of chromodomain of Rhino | ||||||
Components | RE36324p | ||||||
Keywords | PROTEIN BINDING / histone binding | ||||||
Function / homology | Function and homology information piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / piRNA processing / chromosome organization / heterochromatin / pericentric heterochromatin / methylated histone binding ...piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / piRNA processing / chromosome organization / heterochromatin / pericentric heterochromatin / methylated histone binding / transcription antitermination / chromatin organization / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å | ||||||
Authors | Li, S. / Patel, D.J. | ||||||
Citation | Journal: Genes Dev. / Year: 2014 Title: Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Authors: Le Thomas, A. / Stuwe, E. / Li, S. / Du, J. / Marinov, G. / Rozhkov, N. / Chen, Y.C. / Luo, Y. / Sachidanandam, R. / Toth, K.F. / Patel, D. / Aravin, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4quc.cif.gz | 37.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4quc.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 4quc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/4quc ftp://data.pdbj.org/pub/pdb/validation_reports/qu/4quc | HTTPS FTP |
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-Related structure data
Related structure data | 4qufC 1kneS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 7885.945 Da / Num. of mol.: 1 / Fragment: chromodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG10683, Dmel_CG10683, rhi, rhino / Plasmid: pETsumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q7JXA8 |
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#2: 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: 1.85 Å3/Da / Density % sol: 33.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M Sodium nitrate and 20%(w/v) PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.029 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.029 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 9886 / Num. obs: 9293 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 61.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 3.1 / Num. unique all: 811 / Rsym value: 0.653 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KNE Resolution: 1.502→14.589 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.92 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.502→14.589 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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