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- PDB-4pw6: 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: 4pw6 | ||||||
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Title | structure of UHRF2-SRA in complex with a 5hmC-containing DNA, complex II | ||||||
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![]() | LIGASE/DNA / SRA / 5hmC binding / 5hmC-containing DNA / hydroxymethylation / nuclear / LIGASE-DNA complex | ||||||
Function / homology | ![]() SUMO transferase activity / 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 ...SUMO transferase activity / 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 / cell cycle / 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 | ![]() | 100.3 KB | Display | ![]() |
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PDB format | ![]() | 73.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pw5C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 25579.746 Da / Num. of mol.: 2 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: 3747.465 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 3606.381 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris pH 8.0 and 8% PEG-8000, 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: Jun 27, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.51 |
Reflection | Resolution: 3.789→50 Å / Num. all: 5589 / Num. obs: 5480 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 3.789→3.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.8 / Num. unique all: 536 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3OLN Resolution: 3.789→38.674 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.52 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.5 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.789→38.674 Å
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Refine LS restraints |
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LS refinement shell |
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