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Open data
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Basic information
Entry | Database: PDB / ID: 5zu1 | ||||||
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Title | Crystal Structure of BZ junction in diverse sequence | ||||||
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![]() | HYDROLASE/DNA / ![]() ![]() | ||||||
Function / homology | ![]() somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing ...somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / hematopoietic stem cell homeostasis / response to interferon-alpha / adenosine to inosine editing / RISC complex assembly / pre-miRNA processing / negative regulation of hepatocyte apoptotic process / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / positive regulation of viral genome replication / hematopoietic progenitor cell differentiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, K.K. / Kim, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Sequence preference and structural heterogeneity of BZ junctions. Authors: Kim, D. / Hur, J. / Han, J.H. / Ha, S.C. / Shin, D. / Lee, S. / Park, S. / Sugiyama, H. / Kim, K.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.6 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zuoC ![]() 5zupC ![]() 2acjS 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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Unit cell |
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Components
#1: Protein | Mass: 6957.144 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P55265, double-stranded RNA adenine deaminase #2: DNA chain | | Mass: 5148.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 5268.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.69 % / Mosaicity: 0.482 ° |
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Crystal grow![]() | Temperature: 296 K / Method: batch mode / pH: 4.5 Details: 25% 2-methyl-2,4-pentanediol (MPD), 100mM NaOAC, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 4, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→20 Å / Num. obs: 8369 / % possible obs: 99.5 % / Redundancy: 10.5 % / Biso Wilson estimate: 97.03 Å2 / Rmerge(I) obs: 0.059 / Χ2: 2.455 / Net I/σ(I): 21.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2ACJ Resolution: 3.009→19.994 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 207.54 Å2 / Biso mean: 98.9135 Å2 / Biso min: 50.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.009→19.994 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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