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Yorodumi- PDB-1qu5: NMR STRUCTURE OF A NEW PHOSPHOTYROSINE BINDING DOMAIN CONTAINING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qu5 | ||||||
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Title | NMR STRUCTURE OF A NEW PHOSPHOTYROSINE BINDING DOMAIN CONTAINING THE FHA2 DOMAIN OF RAD 53 | ||||||
Components | PROTEIN KINASE SPK1 | ||||||
Keywords | TRANSFERASE / FHA / RAD53 | ||||||
Function / homology | Function and homology information deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / negative regulation of phosphorylation / dual-specificity kinase / DNA replication origin binding / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity ...deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / negative regulation of phosphorylation / dual-specificity kinase / DNA replication origin binding / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / protein localization / protein tyrosine kinase activity / protein kinase activity / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS | ||||||
Model type details | minimized average | ||||||
Authors | Byeon, I.-J.L. / Liao, H. / Tsai, M.-D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Structure and function of a new phosphopeptide-binding domain containing the FHA2 of Rad53. Authors: Liao, H. / Byeon, I.J. / Tsai, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qu5.cif.gz | 931.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qu5.ent.gz | 777.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/1qu5 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/1qu5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20936.861 Da / Num. of mol.: 1 / Fragment: PHOSPHOTYROSINE-BINDING FHA2 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P22216, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURAL DETERMINATION WAS BENEFITED BY THE TROSY TYPE EXPERIMENTS ON THE TRIPLE-LABLED (13C, 15N, 2H) SAMPLE. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 0.2 / pH: 6.5 / Pressure: AMBIENT / Temperature: 293 K | ||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1 Details: IN THE FIRST STAGE, THE SIMULATED ANNEALING STRUCTURES WERE DETERMINED BASED ON THE EXPERIMENTAL INTER PROTON DISTANCE RESTRAINTS (2651 IN TOTAL). THE RESULTING STRUCTURES WERE THEN USED AS ...Details: IN THE FIRST STAGE, THE SIMULATED ANNEALING STRUCTURES WERE DETERMINED BASED ON THE EXPERIMENTAL INTER PROTON DISTANCE RESTRAINTS (2651 IN TOTAL). THE RESULTING STRUCTURES WERE THEN USED AS INITIAL STRCUTURES FOR THE SECOND STAGE OF SIMULATED ANNEALING CALCULATIONS WHERE, IN ADDITION TO THE DISTANCE RESTRAINTS, THE STRUCTURES WERE REFINED AGAINST SECONDARY 13C(ALPHA)/13C(BETA) CHEMICAL SHIFT RESTRAINTS. | ||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 32 / Conformers submitted total number: 16 |