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- PDB-1k3j: Refined NMR Structure of the FHA1 Domain of Yeast Rad53 -

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Basic information

Entry
Database: PDB / ID: 1k3j
TitleRefined NMR Structure of the FHA1 Domain of Yeast Rad53
ComponentsProtein Kinase SPK1
KeywordsTRANSFERASE / FHA domain / Rad53 / Rad9 / phosphothreonine / phosphoprotein
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / negative regulation of phosphorylation / dual-specificity kinase / calcium/calmodulin-dependent protein kinase activity / DNA replication origin binding / 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 / calcium/calmodulin-dependent protein kinase activity / 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 / cellular response to oxidative stress / protein tyrosine kinase activity / calmodulin binding / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / 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 / 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. ...Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / 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 / The structures are based on a total of 2377 restraints. Among them, 2107 are NOE-derived distance constraints, 192 TALOS-derived dihedral angle restraints, and 78 restraints from hydrogen bonds.
AuthorsYuan, C. / Yongkiettrakul, S. / Byeon, I.-J.L. / Zhou, S. / Tsai, M.-D.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structures of two FHA1-phosphothreonine peptide complexes provide insight into the structural basis of the ligand specificity of FHA1 from yeast Rad53.
Authors: Yuan, C. / Yongkiettrakul, S. / Byeon, I.J. / Zhou, S. / Tsai, M.D.
History
DepositionOct 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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 Kinase SPK1


Theoretical massNumber of molelcules
Total (without water)17,0931
Polymers17,0931
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 / 50structures with the least restraint violations, structures with the lowest energy
Representative

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Components

#1: Protein Protein Kinase SPK1


Mass: 17093.490 Da / Num. of mol.: 1 / Fragment: N-terminal FHA domain (FHA1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPK1 or Rad53 / 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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 13C-separated NOESY
NMR detailsText: The structure was refined by adding 221 NOE-derived distance constraints and by revising a few previous NOE assignments.

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Sample preparation

DetailsContents: 0.5 mM protein U-15N,13C; 10 mM sodium phosphate buffer (pH 6.5), 1 mM DTT, and 1 mM EDTA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate, 1mM DTT, and 1 mM EDTA
pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
CNS1Brunger et al.structure solution
CNS1Brunger et al.refinement
RefinementMethod: The structures are based on a total of 2377 restraints. Among them, 2107 are NOE-derived distance constraints, 192 TALOS-derived dihedral angle restraints, and 78 restraints from hydrogen bonds.
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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