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- PDB-3q1j: Crystal structure of tudor domain 1 of human PHD finger protein 20 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q1j | ||||||
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Title | Crystal structure of tudor domain 1 of human PHD finger protein 20 | ||||||
![]() | PHD finger protein 20 | ||||||
![]() | TRANSCRIPTION / tudor domain / mbt / structural genomics consortium / SGC | ||||||
Function / homology | ![]() NSL complex / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Stabilization of p53 / Regulation of TP53 Degradation / chromatin organization / HATs acetylate histones / nuclear membrane ...NSL complex / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Stabilization of p53 / Regulation of TP53 Degradation / chromatin organization / HATs acetylate histones / nuclear membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tempel, W. / Li, Z. / Wernimont, A.K. / Chao, X. / Bian, C. / Lam, R. / Crombet, L. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Tempel, W. / Li, Z. / Wernimont, A.K. / Chao, X. / Bian, C. / Lam, R. / Crombet, L. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins. Authors: Adams-Cioaba, M.A. / Li, Z. / Tempel, W. / Guo, Y. / Bian, C. / Li, Y. / Lam, R. / 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 | ![]() | 27.2 KB | Display | ![]() |
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PDB format | ![]() | 16.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.7 KB | Display | ![]() |
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Full document | ![]() | 418.7 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qiiC ![]() 2eqmS ![]() 2rhuS 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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1 | ![]()
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Unit cell |
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Details | biological unit was not experimentally determined. |
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Components
#1: Protein | Mass: 8211.169 Da / Num. of mol.: 1 / Fragment: residues 1-81 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain (production host): BL21 (DE3) Codon plus RIL (Stratagene) References: UniProt: Q9BVI0 |
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#2: Chemical | ChemComp-UNX / |
#3: Water | ChemComp-HOH / |
Sequence details | THE INITIAL SEQUENCE OF THE PROTEIN HAS THE FOLLOWING SEQUENCE, ...THE INITIAL SEQUENCE OF THE PROTEIN HAS THE FOLLOWING SEQUENCE, MHHHHHHSSR |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG-3350, 0.2M ammonium acetate, 0.1M bis-tris. Prior to freezing, a cluster of thin rods was transferred to a drop of paratone oil. A fragment of the cluster was frozen in a stream of ...Details: 25% PEG-3350, 0.2M ammonium acetate, 0.1M bis-tris. Prior to freezing, a cluster of thin rods was transferred to a drop of paratone oil. A fragment of the cluster was frozen in a stream of cold nitrogen., pH 5.5, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 6, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→20 Å / Num. obs: 2828 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Χ2: 1.927 / Net I/σ(I): 9.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entries 2rhu, 2eqm Resolution: 2.35→19.08 Å / Cor.coef. Fo:Fc: 0.9033 / Cor.coef. Fo:Fc free: 0.8819 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 Details: The programs molrep, chainsaw, phenix, refmac, coot and the ffas03 and molprobity servers where also used in the course of refinement
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Displacement parameters | Biso max: 109.13 Å2 / Biso mean: 43.4265 Å2 / Biso min: 25.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.307 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→19.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.63 Å / Total num. of bins used: 5
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