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Yorodumi- PDB-6at0: Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at posit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6at0 | ||||||
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Title | Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone H3 peptide containing trimethyl lysine | ||||||
Components |
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Keywords | TRANSCRIPTION / histone reader | ||||||
Function / homology | Function and homology information protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / satellite DNA binding / positive regulation of DNA methylation-dependent heterochromatin formation / pericentric heterochromatin formation / chromocenter / polytene chromosome / rDNA binding / condensed chromosome, centromeric region / regulation of protein localization to chromatin / RNA polymerase binding / nucleosomal DNA binding / RNA polymerase II C-terminal domain binding / chromosome, centromeric region / chromosome organization / heterochromatin / pericentric heterochromatin / heterochromatin formation / condensed chromosome / Hsp70 protein binding / methylated histone binding / telomere maintenance / euchromatin / nucleosome assembly / structural constituent of chromatin / nucleosome / protein-macromolecule adaptor activity / mitotic cell cycle / chromosome / chromatin organization / histone binding / chromosome, telomeric region / protein heterodimerization activity / negative regulation of gene expression / mRNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive 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: 1.285 Å | ||||||
Authors | Brustad, E.M. / Baril, S.A. / Waters, M.L. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis. Authors: Baril, S.A. / Koenig, A.L. / Krone, M.W. / Albanese, K.I. / He, C.Q. / Lee, G.Y. / Houk, K.N. / Waters, M.L. / Brustad, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6at0.cif.gz | 29.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6at0.ent.gz | 17.1 KB | Display | PDB format |
PDBx/mmJSON format | 6at0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6at0 ftp://data.pdbj.org/pub/pdb/validation_reports/at/6at0 | HTTPS FTP |
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-Related structure data
Related structure data | 6aszC 1kneS S: Starting model for refinement C: citing same article (ref.) |
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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: 8615.466 Da / Num. of mol.: 1 / Fragment: Chromo 1 domain, residues 17-76 / Mutation: K38M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Su(var)205, HP1, CG8409 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P05205 |
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#2: Protein/peptide | Mass: 733.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P02299*PLUS |
#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: 2.7 Å3/Da / Density % sol: 54.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.1M MES, 3.0M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.285→11.224 Å / Num. obs: 25429 / % possible obs: 96.9 % / Redundancy: 5.36 % / Net I/σ(I): 12.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KNE Resolution: 1.285→11.224 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 39.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.3 Å2 / Biso mean: 28.7653 Å2 / Biso min: 13.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.285→11.224 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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