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Yorodumi- PDB-3h91: Crystal structure of the complex of human chromobox homolog 2 (CB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h91 | ||||||
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Title | Crystal structure of the complex of human chromobox homolog 2 (CBX2) and H3K27 peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / human chromobox homolog 2 / CBX2 / H3K27 / Structural Genomics / Structural Genomics Consortium / SGC / Chromatin regulator / DNA-binding / Nucleus / Repressor / Transcription regulation | ||||||
Function / homology | Function and homology information development of primary sexual characteristics / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / heterochromatin / SUMOylation of DNA damage response and repair proteins / methylated histone binding / SUMOylation of chromatin organization proteins ...development of primary sexual characteristics / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / heterochromatin / SUMOylation of DNA damage response and repair proteins / methylated histone binding / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / euchromatin / structural constituent of chromatin / nucleosome / chromatin organization / Oxidative Stress Induced Senescence / cell differentiation / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Amaya, M.F. / Ravichandran, M. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. ...Amaya, M.F. / Ravichandran, M. / 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 | 3h91.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h91.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 3h91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/3h91 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/3h91 | HTTPS FTP |
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-Related structure data
Related structure data | 2l11C 2l12C 2l1bC 3fdtC 3gv6C 3i90C 3i91C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6511.553 Da / Num. of mol.: 2 / Fragment: UNP residues 9-62 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBX2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14781 #2: Protein/peptide | Mass: 1515.776 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: Q92133*PLUS #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: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG3350, 0.1 M Tris, pH8.5, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||||||
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Detector | Date: Jan 21, 2009 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. obs: 26030 / % possible obs: 93.8 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 38.995 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.204 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.075 / 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: 16.163 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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