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Yorodumi- PDB-3qby: Crystal structure of the PWWP domain of human Hepatoma-derived gr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qby | ||||||
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Title | Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2 | ||||||
Components |
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Keywords | PROTEIN BINDING / hdgf2 / structural genomics consortium / SGC | ||||||
Function / homology | Function and homology information H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / DNA repair-dependent chromatin remodeling / muscle organ development / histone reader activity / positive regulation of double-strand break repair via homologous recombination / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity ...H3K27me3 modified histone binding / H3K9me3 modified histone binding / skeletal muscle tissue regeneration / muscle cell differentiation / DNA repair-dependent chromatin remodeling / muscle organ development / histone reader activity / positive regulation of double-strand break repair via homologous recombination / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / methylated histone binding / positive regulation of cell growth / DNA recombination / chromatin remodeling / DNA repair / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Zeng, H. / Tempel, W. / Amaya, M.F. / Adams-Cioaba, M.A. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. ...Zeng, H. / Tempel, W. / Amaya, M.F. / Adams-Cioaba, M.A. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Structural and Histone Binding Ability Characterizations of Human PWWP Domains. Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Amaya, M.F. / Xu, C. / Dombrovski, L. / Qiu, W. / 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 | 3qby.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qby.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qby_validation.pdf.gz | 471.4 KB | Display | wwPDB validaton report |
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Full document | 3qby_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 3qby_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3qby_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/3qby ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qby | HTTPS FTP |
-Related structure data
Related structure data | 3eaeSC 3l42C 3llrC 3lyiC 3mo8C 3pfsC 3pmiC 3qj6C 3qkjC 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: 10714.236 Da / Num. of mol.: 3 / Fragment: UNP residues 1-93 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFRP2, HDGF2, UNQ785/PRO1604 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2R-pRARE / References: UniProt: Q7Z4V5 #2: Protein/peptide | | Mass: 1440.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P62805*PLUS #3: Chemical | ChemComp-UNX / #4: Chemical | #5: 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: 2.1 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 4.6 Details: 2.5 M ammonium sulfate, 0.1 M sodium acetate, peptide ligand was added at 0.005 M concentration, pH 4.6, vapor diffusion, temperature 291K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 3, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→25 Å / Num. obs: 21026 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.039 / Χ2: 1.738 / Net I/σ(I): 23.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3EAE Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.226 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.598 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED.
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.98 Å2 / Biso mean: 33.681 Å2 / Biso min: 14.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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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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