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Yorodumi- PDB-2qic: Crystal Structure of the ING1 PHD Finger in complex with a Histon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qic | ||||||
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Title | Crystal Structure of the ING1 PHD Finger in complex with a Histone H3K4ME3 peptide | ||||||
Components |
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Keywords | ANTITUMOR PROTEIN / APOPTOSIS / PHD / ING1 / HISTONE / H3K4ME3 / CHROMATIN | ||||||
Function / homology | Function and homology information regulation of response to osmotic stress / phosphorelay sensor kinase activity / plasma membrane => GO:0005886 / phosphorelay signal transduction system Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Rigid Body Refinement / Resolution: 2.1 Å | ||||||
Authors | Pena, P.V. / Champagne, K. / Zhao, R. / Kutateladze, T.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor. Authors: Pena, P.V. / Hom, R.A. / Hung, T. / Lin, H. / Kuo, A.J. / Wong, R.P. / Subach, O.M. / Champagne, K.S. / Zhao, R. / Verkhusha, V.V. / Li, G. / Gozani, O. / Kutateladze, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qic.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qic.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qic_validation.pdf.gz | 429.7 KB | Display | wwPDB validaton report |
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Full document | 2qic_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 2qic_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 2qic_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/2qic ftp://data.pdbj.org/pub/pdb/validation_reports/qi/2qic | HTTPS FTP |
-Related structure data
Related structure data | 2g6qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 7075.926 Da / Num. of mol.: 1 / Fragment: PHD DOMAIN (RESIDUES 345-404) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ING1 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9UK53 | ||
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#2: Protein/peptide | Mass: 1350.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic PEPTIDE H3K4ME3 | ||
#3: Chemical | #4: 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: 2.17 Å3/Da / Density % sol: 43.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.01 M NiCl2 6H20, 0.1 M Tris, 20% polyethylene glycol monomethyl ether 2K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.257 Å |
Detector | Detector: AREA DETECTOR / Date: Feb 26, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.257 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 4526 / Num. obs: 4526 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 9.35 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 9.78 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.4 / Num. unique all: 450 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid Body Refinement Starting model: PDB entry 2G6Q Resolution: 2.1→25 Å
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å
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