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Yorodumi- PDB-4x3s: Crystal structure of chromobox homology 7 (CBX7) with SETDB1-1170... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x3s | ||||||
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Title | Crystal structure of chromobox homology 7 (CBX7) with SETDB1-1170me3 Peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / CBX7 / chromodomain | ||||||
Function / homology | Function and homology information [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / sebaceous gland development / histone H3K9 monomethyltransferase activity / PRC1 complex / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / PcG protein complex ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / sebaceous gland development / histone H3K9 monomethyltransferase activity / PRC1 complex / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / PcG protein complex / heterochromatin / heterochromatin organization / methylated histone binding / promoter-specific chromatin binding / positive regulation of transcription elongation by RNA polymerase II / PKMTs methylate histone lysines / chromatin organization / chromosome / methylation / single-stranded RNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Ren, C. / Plotnikov, A.N. / Zhou, M.M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2015 Title: Small-Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain. Authors: Ren, C. / Morohashi, K. / Plotnikov, A.N. / Jakoncic, J. / Smith, S.G. / Li, J. / Zeng, L. / Rodriguez, Y. / Stojanoff, V. / Walsh, M. / Zhou, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x3s.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x3s.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 4x3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x3s_validation.pdf.gz | 455.2 KB | Display | wwPDB validaton report |
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Full document | 4x3s_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 4x3s_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 4x3s_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/4x3s ftp://data.pdbj.org/pub/pdb/validation_reports/x3/4x3s | HTTPS FTP |
-Related structure data
Related structure data | 4x3kC 4x3tC 4x3uC 3i91S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 7730.877 Da / Num. of mol.: 2 / Fragment: UNP residues 7-66 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbx7, D15Ertd417e / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDS3 #2: Protein/peptide | Mass: 1118.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15047*PLUS #3: Chemical | #4: Chemical | ChemComp-CIT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 10% Jeffamine M-600, 0.1 M Na Citrate pH 5.6, 0.01 M FeCl3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.4 Å / Num. obs: 23204 / % possible obs: 99.36 % / Redundancy: 4.6 % / Net I/σ(I): 42.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I91 Resolution: 1.6→23.26 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.606 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.093 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.087 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→23.26 Å
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