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- PDB-4pw5: structure of UHRF2-SRA in complex with a 5hmC-containing DNA, com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pw5 | ||||||
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Title | structure of UHRF2-SRA in complex with a 5hmC-containing DNA, complex I | ||||||
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![]() | LIGASE/DNA / SRA / 5hmC binding / 5hmC-containing DNA / hydroxymethylation / nuclear / LIGASE-DNA complex | ||||||
Function / homology | ![]() SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / protein autoubiquitination / heterochromatin / pericentric heterochromatin / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity ...SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / protein autoubiquitination / heterochromatin / pericentric heterochromatin / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / regulation of cell cycle / protein ubiquitination / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | ZHou, T. / Xiong, J. / Wang, M. / Yang, N. / Wong, J. / Zhu, B. / Xu, R.M. | ||||||
![]() | ![]() Title: Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2. Authors: Zhou, T. / Xiong, J. / Wang, M. / Yang, N. / Wong, J. / Zhu, B. / Xu, R.M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.9 KB | Display | ![]() |
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PDB format | ![]() | 156.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pw6C ![]() 4pw7C ![]() 3olnS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25579.746 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96PU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: DNA chain | Mass: 3724.428 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 3592.358 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% ethanol and 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 56609 / Num. obs: 54600 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.483 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3OLN Resolution: 2.204→41.432 Å / SU ML: 0.23 / Isotropic thermal model: 31.2 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.03 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.204→41.432 Å
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Refine LS restraints |
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LS refinement shell |
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