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Yorodumi- PDB-1ujx: The forkhead associated (FHA) domain like structure from mouse po... -
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-Basic information
Entry | Database: PDB / ID: 1ujx | ||||||
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Title | The forkhead associated (FHA) domain like structure from mouse polynucleotide kinase 3'-phosphatase | ||||||
Components | polynucleotide kinase 3'-phosphatase | ||||||
Keywords | HYDROLASE / TRANSFERASE / DNA REPAIR / FHA domain / polynucleotide kinase 3'-phosphatase / beta-sandwich / antiparallel beta-sheets / phosphopeptide binding motif / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping ...polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping / ubiquitin-like ligase-substrate adaptor activity / positive regulation of telomere maintenance via telomerase / double-strand break repair via nonhomologous end joining / site of double-strand break / double-stranded DNA binding / response to oxidative stress / phosphorylation / DNA repair / DNA damage response / nucleolus / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: The forkhead associated (FHA) domain like structure from mouse polynucleotide kinase 3'-phosphatase Authors: Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ujx.cif.gz | 676.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ujx.ent.gz | 566.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ujx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/1ujx ftp://data.pdbj.org/pub/pdb/validation_reports/uj/1ujx | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12322.932 Da / Num. of mol.: 1 / Fragment: FHA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1810009G08 / Plasmid: P030107-24 References: UniProt: Q9JLV6, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.16mM FHA domain U-15N, 13C; 20mM phosphate Na(pH 6.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |