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- PDB-1dmz: A REFINED NMR STRUCTURE OF A NEW PHOPHOPEPTIDE-BINDING DOMAIN CON... -

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Basic information

Entry
Database: PDB / ID: 1dmz
TitleA REFINED NMR STRUCTURE OF A NEW PHOPHOPEPTIDE-BINDING DOMAIN CONTAINING THE FHA2 OF RAD53
ComponentsPROTEIN (PROTEIN KINASE SPK1)
KeywordsTRANSFERASE / BETA-SANDWICH / ANTIPARALLEL BETA-SHEETS
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling ...deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / intracellular protein localization / protein tyrosine kinase activity / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site ...Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsByeon, I.-J.L. / Liao, H. / Tsai, M.-D.
CitationJournal: 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
DepositionDec 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PROTEIN KINASE SPK1)


Theoretical massNumber of molelcules
Total (without water)18,1491
Polymers18,1491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 35structures with the lowest energy
RepresentativeModel #20

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Components

#1: Protein PROTEIN (PROTEIN KINASE SPK1)


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C-SEPARATED NOESY
1213D 15N-SEPARATED NOESY
1313D 13C-SEPARATED NOESY
1413D 13C-SEPARATED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 0.2-0.5 MM FHA2 U-15N, 13C; 10 MM SODIUM PHOSPHATE, 1 MM DTT, 1 MM EDTA
Sample conditionsIonic strength: 0.01 / pH: 6.5 / Pressure: AMBIENT / Temperature: 293.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
TALOS98.040.21.02GABRIEL CORNILESCU, FRANK DELAGLIO,refinement
X-PLOR X-PLOR (ONLINE)3.851structure solution
RefinementMethod: 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 ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 20

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