+Open data
-Basic information
Entry | Database: PDB / ID: 5ikj | ||||||
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Title | Structure of Clr2 bound to the Clr1 C-terminus | ||||||
Components |
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Keywords | TRANSCRIPTION / Methyl-CpG-binding domain / BAH domain / chromobarrel domain / complex / Cell cycle | ||||||
Function / homology | Function and homology information SHREC complex / : / CENP-A containing chromatin / : / mating-type region heterochromatin / heterochromatin formation => GO:0031507 / chromosome, subtelomeric region / rDNA heterochromatin / silent mating-type cassette heterochromatin formation / pericentric heterochromatin ...SHREC complex / : / CENP-A containing chromatin / : / mating-type region heterochromatin / heterochromatin formation => GO:0031507 / chromosome, subtelomeric region / rDNA heterochromatin / silent mating-type cassette heterochromatin formation / pericentric heterochromatin / heterochromatin formation / chromatin organization / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Pfister, Y. / Schalch, T. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Mol.Cell / Year: 2016 Title: SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules. Authors: Job, G. / Brugger, C. / Xu, T. / Lowe, B.R. / Pfister, Y. / Qu, C. / Shanker, S. / Banos Sanz, J.I. / Partridge, J.F. / Schalch, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ikj.cif.gz | 208.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ikj.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ikj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ikj_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 5ikj_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 5ikj_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5ikj_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5ikj ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5ikj | HTTPS FTP |
-Related 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: 63119.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: T7-tagged Clr2 full length Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Gene: clr2, SPAC1B3.17 / Plasmid: p724 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O13881 | ||
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#2: Protein | Mass: 9719.022 Da / Num. of mol.: 1 / Fragment: UNP residues 1151-1238 Source method: isolated from a genetically manipulated source Details: Clr1 residues 1151-1238 Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: clr1, SPBC2D10.17 / Plasmid: p724 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O74808 | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: 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: 2.87 Å3/Da / Density % sol: 57.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 0.1 M Tris-bicine 30 mM Sodium Fluoride 30 mM Sodium Bromide 30 mM Sodium Iodide 18% Ethylene glycol 9% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763,0.9792,0.9763,0.9792 | |||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2013 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→48.325 Å / Num. obs: 37719 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 54.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 24.9 | |||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→48.325 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 28.9 / 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: 2.3→48.325 Å
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Refine LS restraints |
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LS refinement shell |
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