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- PDB-7c4p: Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c4p | ||||||
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Title | Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA | ||||||
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![]() | DNA BINDING PROTEIN / zebrafish TRF2 / telomeric DNA / complex. | ||||||
Function / homology | ![]() negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / G-rich strand telomeric DNA binding ...negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / G-rich strand telomeric DNA binding / protein localization to chromosome, telomeric region / cell cycle / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, Z. / Park, J.H. / Yun, J.H. / Park, S.Y. / Lee, W. | ||||||
![]() | ![]() Title: Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA Authors: Jin, Z. / Park, J.H. / Yun, J.H. / Park, S.Y. / Lee, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.1 KB | Display | ![]() |
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PDB format | ![]() | 42.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.8 KB | Display | ![]() |
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Full document | ![]() | 447.8 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c4qC ![]() 1w0uS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 6684.843 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein | Mass: 6620.800 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-DNA chain , 3 types, 4 molecules CDFE
#2: DNA chain | Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
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#3: DNA chain | Mass: 3551.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #5: DNA chain | | Mass: 3115.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 1 types, 59 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 20-25% (w/v) polyethylene glycol 3000, 100 mM Sodium acetate/acetic acid |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9946→43.736 Å / Num. obs: 23161 / % possible obs: 97.56 % / Redundancy: 4.9 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 26.86 |
Reflection shell | Resolution: 1.995→2.045 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1368 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1W0U Resolution: 1.995→43.736 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.99 Å2 / Biso mean: 42.651 Å2 / Biso min: 26.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.995→43.736 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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