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Open data
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Basic information
Entry | Database: PDB / ID: 3pu3 | ||||||
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Title | PHF2 Jumonji domain-NOG complex | ||||||
![]() | PHD finger protein 2 | ||||||
![]() | PROTEIN BINDING / alpha-ketoglutarate-Fe2+ dependent dioxygenases / Histone Tail BINDING PROTEIN | ||||||
Function / homology | ![]() histone H4K20 demethylase activity / negative regulation of rDNA heterochromatin formation / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / protein demethylation / histone H3K9 demethylase activity / transcription initiation-coupled chromatin remodeling / methylated histone binding / liver development / transcription coregulator activity / HDMs demethylate histones ...histone H4K20 demethylase activity / negative regulation of rDNA heterochromatin formation / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / protein demethylation / histone H3K9 demethylase activity / transcription initiation-coupled chromatin remodeling / methylated histone binding / liver development / transcription coregulator activity / HDMs demethylate histones / kinetochore / transcription coactivator activity / iron ion binding / nucleolus / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horton, J.R. / Upadhyay, A.K. / Hashimoto, H. / Zhang, X. / Cheng, X. | ||||||
![]() | ![]() Title: Structural basis for human PHF2 Jumonji domain interaction with metal ions. Authors: Horton, J.R. / Upadhyay, A.K. / Hashimoto, H. / Zhang, X. / Cheng, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172 KB | Display | ![]() |
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PDB format | ![]() | 133.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.4 KB | Display | ![]() |
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Full document | ![]() | 482.7 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ptrC ![]() 3pu8C ![]() 3puaC ![]() 3pusC ![]() 3kv4S C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44715.215 Da / Num. of mol.: 2 / Fragment: Jumonji domain (unp residues 60-451) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.8 % |
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Crystal grow | Method: vapor diffusion / pH: 6 Details: 18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→31.18 Å / Num. obs: 60290 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 20.85 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5989 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3KV4 Resolution: 1.95→31.18 Å / SU ML: 0.32 / σ(F): 0.05 / Phase error: 30.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.617 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.95→31.18 Å
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Refine LS restraints |
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LS refinement shell |
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