+Open data
-Basic information
Entry | Database: PDB / ID: 3p7j | ||||||
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Title | Drosophila HP1a chromo shadow domain | ||||||
Components | Heterochromatin protein 1 | ||||||
Keywords | TRANSCRIPTION / heterochromatin protein 1 / chromo shadow domain / gene silencing / epigenetics | ||||||
Function / homology | Function and homology information protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / satellite DNA binding / : / positive regulation of DNA methylation-dependent heterochromatin formation / chromocenter / pericentric heterochromatin formation / polytene chromosome ...protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / satellite DNA binding / : / positive regulation of DNA methylation-dependent heterochromatin formation / chromocenter / pericentric heterochromatin formation / polytene chromosome / rDNA binding / condensed chromosome, centromeric region / regulation of protein localization to chromatin / RNA polymerase binding / RNA polymerase II C-terminal domain binding / chromosome, centromeric region / chromosome organization / heterochromatin / pericentric heterochromatin / heterochromatin formation / condensed chromosome / methylated histone binding / telomere maintenance / Hsp70 protein binding / euchromatin / protein-macromolecule adaptor activity / mitotic cell cycle / chromosome / chromatin organization / histone binding / chromosome, telomeric region / negative regulation of gene expression / mRNA binding / negative regulation of DNA-templated transcription / chromatin binding / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kim, D. / Chruszcz, M. / Minor, W. / Khorasanizadeh, S. | ||||||
Citation | Journal: Chembiochem / Year: 2011 Title: The HP1a Disordered C Terminus and Chromo Shadow Domain Cooperate to Select Target Peptide Partners. Authors: Mendez, D.L. / Kim, D. / Chruszcz, M. / Stephens, G.E. / Minor, W. / Khorasanizadeh, S. / Elgin, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p7j.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p7j.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 3p7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/3p7j ftp://data.pdbj.org/pub/pdb/validation_reports/p7/3p7j | HTTPS FTP |
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-Related structure data
Related structure data | 2fmmS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10035.203 Da / Num. of mol.: 2 / Fragment: UNP residues 131-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Su(var)205, HP1, CG8409 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: P05205 #2: Chemical | ChemComp-GOL / | #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: 2.12 Å3/Da / Density % sol: 42.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG400, 0.1 M HEPES. Cryoprotected in 12% PEG400, 0.1 M HEPES, 33% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2009 / Details: mirror |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 8023 / Num. obs: 8023 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.3 / Num. unique all: 397 / Rsym value: 0.475 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FMM Resolution: 2.3→31.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.616 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.534 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→31.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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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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