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- PDB-1g3g: NMR STRUCTURE OF THE FHA1 DOMAIN OF YEAST RAD53 -

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Basic information

Entry
Database: PDB / ID: 1g3g
TitleNMR STRUCTURE OF THE FHA1 DOMAIN OF YEAST RAD53
ComponentsPROTEIN KINASE SPK1
KeywordsTRANSFERASE / FHA domain / Rad53 / Phosphopeptide / Phosphoprotein
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
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 / simulated annealing
AuthorsYuan, C. / Liao, H. / Su, M. / Yongkiettrakul, S. / Byeon, I.-J.L. / Tsai, M.-D.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structure of the FHA1 domain of yeast Rad53 and identification of binding sites for both FHA1 and its target protein Rad9
Authors: Liao, H. / Yuan, C. / Su, M.I. / Yongkiettrakul, S. / Qin, D. / Li, H. / Byeon, I.J. / Pei, D. / Tsai, M.D.
History
DepositionOct 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Sep 2, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _entity.pdbx_description / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)18,5071
Polymers18,5071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #2closest to the average

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Components

#1: Protein PROTEIN KINASE SPK1 / SERINE-PROTEIN KINASE 1


Mass: 18506.938 Da / Num. of mol.: 1 / Fragment: THE N-TERMINAL FHA DOMAIN (FHA1), RESIDUES 1-164 / Mutation: M1G
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 experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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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; 95 % H2O, 5 % D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate, 1 mM DTT, and 1 mM EDTA
pH: 6.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2156 restraints, 1886 are NOE-derived distance constraints, 192 TALOS-derived dihedral angle restraints,78 distance restraints from hydrogen bonds. ...Details: The structures are based on a total of 2156 restraints, 1886 are NOE-derived distance constraints, 192 TALOS-derived dihedral angle restraints,78 distance restraints from hydrogen bonds. RESIDUES 1-14 ARE POORLY DEFINED BY THE EXPERIMENTAL DATA. THUS, NO MEANING SHOULD BE GIVEN TO THOSE RESIDUES' COORDINATES.
NMR representativeSelection criteria: closest to the average
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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