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Yorodumi- PDB-3gv6: Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gv6 | ||||||
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Title | Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide | ||||||
Components |
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Keywords | Transcription/DNA binding protein / chromobox homolog / CBX6 / H3K9 peptide / SGC / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / Chromosomal protein / DNA-binding / Nucleosome core / Transcription-DNA binding protein COMPLEX / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information PRC1 complex / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / heterochromatin / methylated histone binding / Regulation of PTEN gene transcription / structural constituent of chromatin / nucleosome / chromatin organization / Oxidative Stress Induced Senescence ...PRC1 complex / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / heterochromatin / methylated histone binding / Regulation of PTEN gene transcription / structural constituent of chromatin / nucleosome / chromatin organization / Oxidative Stress Induced Senescence / single-stranded RNA binding / nuclear body / protein heterodimerization activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Dong, A. / Amaya, M.F. / Li, Z. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Dong, A. / Amaya, M.F. / Li, Z. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Recognition and specificity determinants of the human cbx chromodomains. Authors: Kaustov, L. / Ouyang, H. / Amaya, M. / Lemak, A. / Nady, N. / Duan, S. / Wasney, G.A. / Li, Z. / Vedadi, M. / Schapira, M. / Min, J. / Arrowsmith, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gv6.cif.gz | 27.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gv6.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gv6 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gv6 | HTTPS FTP |
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-Related structure data
Related structure data | 2l11C 2l12C 2l1bC 3fdtC 3h91C 3i90C 3i91C 3dm1S 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
#1: Protein | Mass: 7137.208 Da / Num. of mol.: 1 / Fragment: UNP residues 8-65 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBX6 / Plasmid: P28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95503 |
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#2: Protein/peptide | Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: UNP residues 2-16 / Source method: obtained synthetically / Details: This sequence occurs naturally in Xenopus laevis / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133, UniProt: P84233*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: 1.73 Å3/Da / Density % sol: 29.03 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 14% PEG 3350, 0.2M MgCl2, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 3, 2009 / Details: VeriMax HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. all: 6339 / Num. obs: 6339 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.66 / Num. unique all: 547 / Rsym value: 0.473 / % possible all: 89.2 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DM1 Resolution: 1.76→24.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.142 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.151 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.219 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→24.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.807 Å / Total num. of bins used: 20
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