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Yorodumi- PDB-6v2r: Crystal Structure of chromodomain of CBX7 mutant V13A in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v2r | ||||||
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Title | Crystal Structure of chromodomain of CBX7 mutant V13A in complex with inhibitor UNC3866 | ||||||
Components |
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Keywords | GENE REGULATION / structural genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information PRC1 complex / PcG protein complex / chromatin organization / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Liu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Liu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell Chem Biol / Year: 2020 Title: Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Authors: Dong, C. / Liu, Y. / Lyu, T.J. / Beldar, S. / Lamb, K.N. / Tempel, W. / Li, Y. / Li, Z. / James, L.I. / Qin, S. / Wang, Y. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v2r.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v2r.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 6v2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v2r_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 6v2r_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 6v2r_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 6v2r_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/6v2r ftp://data.pdbj.org/pub/pdb/validation_reports/v2/6v2r | HTTPS FTP |
-Related structure data
Related structure data | 2mj8C 6v2dC 6v2hC 6v2sC 6v3nC 6v41C 6v8wC 5epjS 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: 6788.799 Da / Num. of mol.: 1 / Fragment: Chromodomain / Mutation: V13A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBX7 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V2R-pRARE2 / References: UniProt: O95931 | ||||
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#2: Protein/peptide | | ||||
#3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.5 M ammonium sulfate, 0.1 M bis-tris propane, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 15, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.57→23.46 Å / Num. obs: 10074 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 15.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.042 / Net I/σ(I): 43 | ||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: isomorphous to PDB entry 5EPJ Resolution: 1.6→23.46 Å / SU ML: 0.1378 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.6482 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→23.46 Å
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Refine LS restraints |
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LS refinement shell |
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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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