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- PDB-1qu5: NMR STRUCTURE OF A NEW PHOSPHOTYROSINE BINDING DOMAIN CONTAINING ... -

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Basic information

Entry
Database: PDB / ID: 1qu5
TitleNMR STRUCTURE OF A NEW PHOSPHOTYROSINE BINDING DOMAIN CONTAINING THE FHA2 DOMAIN OF RAD 53
ComponentsPROTEIN KINASE SPK1
KeywordsTRANSFERASE / FHA / RAD53
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 / cytosol / cytoplasm
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, MOLECULAR DYNAMICS
Model type detailsminimized average
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
DepositionJul 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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)20,9371
Polymers20,9371
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)16 / 32structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein PROTEIN KINASE SPK1


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1213D 15N-SEPARATED NOESY
1314D 13C-SEPARATED NOESY
141(H)CCH-TOCSY
15215N-1H-TROSY-HN(CO)CACB
16215N-1H-TROSY-HN(CA)CB
NMR detailsText: THE STRUCTURAL DETERMINATION WAS BENEFITED BY THE TROSY TYPE EXPERIMENTS ON THE TRIPLE-LABLED (13C, 15N, 2H) SAMPLE.

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Sample preparation

Details
Solution-IDContents
10.2~0.5 MM FHA2, U-15N, 13C; 100 MM SODIUM PHOSPHATE, 1MM DTT, 1MM EDTA
20.2~0.5 MM FHA2, U-15N, 13C, 2H (~70%) TRIPLE LABELED; 100 MM PHOSPHATE, 1MM DTT, 1MM EDTA
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: AMBIENT / Temperature: 293 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
X-PLOR3.1BRUNGER, A. T.refinement
XwinNMR2.1BRUKERstructure solution
Felix98MSIstructure solution
RefinementMethod: 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 representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 32 / Conformers submitted total number: 16

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