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- PDB-3pfs: PWWP Domain of Human Bromodomain and PHD finger-containing protein 3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pfs | ||||||
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Title | PWWP Domain of Human Bromodomain and PHD finger-containing protein 3 | ||||||
![]() | Bromodomain and PHD finger-containing protein 3 | ||||||
![]() | PROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC / PWWP Domain | ||||||
Function / homology | ![]() : / : / : / platelet degranulation / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / positive regulation of DNA replication / Platelet degranulation / HATs acetylate histones ...: / : / : / platelet degranulation / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / positive regulation of DNA replication / Platelet degranulation / HATs acetylate histones / histone binding / extracellular region / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lam, R. / Zeng, H. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.8 KB | Display | ![]() |
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PDB format | ![]() | 92 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.8 KB | Display | ![]() |
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Full document | ![]() | 445.7 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eaeC ![]() 3l42C ![]() 3llrC ![]() 3lyiC ![]() 3mo8C ![]() 3pmiC ![]() 3qbyC ![]() 3qj6C ![]() 3qkjC ![]() 2x4wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18187.018 Da / Num. of mol.: 2 / Fragment: PWWP domain (UNP Residues 1056-1195) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG4000, 0.2M Ammonium Sulfate, 0.1M Sodium Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010 Details: Rosenbaum-Rock high-resolution double-crystal monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→33.631 Å / Num. obs: 22879 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.091 / Χ2: 1.005 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X4W Resolution: 1.9→33.631 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.492 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.71 Å2 / Biso mean: 22.3843 Å2 / Biso min: 8.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→33.631 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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