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Yorodumi- PDB-1dmz: A REFINED NMR STRUCTURE OF A NEW PHOPHOPEPTIDE-BINDING DOMAIN CON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dmz | ||||||
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Title | A REFINED NMR STRUCTURE OF A NEW PHOPHOPEPTIDE-BINDING DOMAIN CONTAINING THE FHA2 OF RAD53 | ||||||
Components | PROTEIN (PROTEIN KINASE SPK1) | ||||||
Keywords | TRANSFERASE / BETA-SANDWICH / ANTIPARALLEL BETA-SHEETS | ||||||
Function / homology | Function and homology information deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / negative regulation of phosphorylation / dual-specificity kinase / DNA replication origin binding / negative regulation of DNA damage checkpoint ...deoxyribonucleoside triphosphate biosynthetic process / G2/M DNA damage checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / meiotic recombination checkpoint signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / negative regulation of phosphorylation / dual-specificity kinase / DNA replication origin binding / 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 / phosphorylation / 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 | ||||||
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 | 1dmz.cif.gz | 992.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dmz.ent.gz | 857 KB | Display | PDB format |
PDBx/mmJSON format | 1dmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dmz ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dmz | 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: 18148.758 Da / Num. of mol.: 1 Fragment: PHOSPHOTYROSINE-BINDING FHA2 DOMAIN (RESIDUES 573-730) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PGEX-4T / Production host: Escherichia coli (E. coli) 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 STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL TRIPLE-RESONANCE NMR SPECTROSCOPY. |
-Sample preparation
Details | Contents: 0.2-0.5 MM FHA2 U-15N, 13C; 10 MM SODIUM PHOSPHATE, 1 MM DTT, 1 MM EDTA |
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Sample conditions | Ionic strength: 0.01 / pH: 6.50 / Pressure: AMBIENT / Temperature: 293.00 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 / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON 2757 DISTANCE RESTRAINTS AND 188 DIHEDRAL ANGLE RESTRAINTS. THE DIHEDRAL ANGLE RESTRAINTS WERE OBTAINED USING TALOS PROGRAM. | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 35 / Conformers submitted total number: 20 |