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- PDB-1i35: SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF THE PROTEIN KINAS... -

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Basic information

Entry
Database: PDB / ID: 1i35
TitleSOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF THE PROTEIN KINASE BYR2 FROM SCHIZOSACCHAROMYCES POMBE
ComponentsPROTEIN KINASE BYR2
KeywordsTRANSFERASE / Ubiquitin superfold
Function / homology
Function and homology information


Oxidative Stress Induced Senescence / induction of conjugation with cellular fusion / pheromone response MAPK cascade / division septum / cell tip / mitogen-activated protein kinase kinase kinase / cell division site / MAP kinase kinase kinase activity / protein kinase activity / protein serine kinase activity ...Oxidative Stress Induced Senescence / induction of conjugation with cellular fusion / pheromone response MAPK cascade / division septum / cell tip / mitogen-activated protein kinase kinase kinase / cell division site / MAP kinase kinase kinase activity / protein kinase activity / protein serine kinase activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / : / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / : / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / High temperature torsion angle dynamics. First cooling stage using torsion angle dynamics. Second cooling stage using Cartesian dynamics. Final energy minimization.
AuthorsGronwald, W. / Huber, F. / Grunewald, P. / Sporner, M. / Wohlgemuth, S. / Herrmann, C. / Kalbitzer, H.R.
Citation
Journal: Structure / Year: 2001
Title: Solution structure of the Ras binding domain of the protein kinase Byr2 from Schizosaccharomyces pombe.
Authors: Gronwald, W. / Huber, F. / Grunewald, P. / Sporner, M. / Wohlgemuth, S. / Herrmann, C. / Kalbitzer, H.R.
#1: Journal: Protein Sci. / Year: 2001
Title: Overcoming the Problems Associated with Poor Spectra Quality of the Protein Kinase Byr2 using Residual Dipolar Couplings
Authors: Gronwald, W. / Brunner, E. / Huber, F. / Wenzler, M. / Herrmann, C. / Kalbitzer, H.R.
#2: Journal: J.Biomol.NMR / Year: 2000
Title: Letter to the Editor: Sequential NMR assignment of the RAS-binding domain of Byr2
Authors: Huber, F. / Gronwald, W. / Wohlgemuth, S. / Herrmann, C. / Geyer, M. / Wittinghofer, A. / Kalbitzer, H.R.
History
DepositionFeb 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 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: 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 KINASE BYR2


Theoretical massNumber of molelcules
Total (without water)10,9881
Polymers10,9881
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)10 / 200The submitted conformer models are the 10 structures with the lowest total energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PROTEIN KINASE BYR2


Mass: 10987.690 Da / Num. of mol.: 1 / Fragment: RAS-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: BYR2 (AMINO ACIDS 71 - 165) / Plasmid: PGEX4T3 (PHARMACIA) / Production host: Escherichia coli (E. coli) / Strain (production host): B121 DE3
References: UniProt: P28829, 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
1112D NOESY
2222D NOESY
3333D 15N-separated NOESY
343HNHA
5553D 13C-separated NOESY
6662D-HSQC with no decoupling of 1H during t1(measurement of residual dipolar couplings)

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM Byr2 unlabeled,25 mM DTE, 200 mM deuterated glycine, 20 mM phosphate buffer, 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM Byr2 unlabeled,25 mM DTE, 200 mM deuterated glycine, 20 mM phosphate buffer, 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM DSS, 100% D2O100% D2O
31.0 mM Byr2 15N-labeled,25 mM DTE, 200 mM deuterated glycine, 20 mM phosphate buffer, 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM Byr2 15N-13C-labeled,25 mM DTE, 200 mM deuterated glycine, 20 mM phosphate buffer, 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
50.7 mM Byr2 15N-13C-labeled,25 mM DTE, 200 mM deuterated glycine, 20 mM phosphate buffer, 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM DSS, 100% D2O100% D2O
61.0 mM Byr2 15N-labeled,25 mM DTE, 200 mM deuterated glycine, 20 mM phosphate buffer, 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM DSS, 5 wt.-% phospholipid bicelles, 90% H2O/10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200 mM deuterated glycine, 20 mM phosphate buffer 6.9ambient 298 K
2200 mM deuterated glycine, 20 mM phosphate buffer 6.9ambient 298 K
3200 mM deuterated glycine, 20 mM phosphate buffer 6.9ambient 298 K
4200 mM deuterated glycine, 20 mM phosphate buffer 6.9ambient 298 K
5200 mM deuterated glycine, 20 mM phosphate buffer 6.9ambient 298 K
6200 mM deuterated glycine, 20 mM phosphate buffer 6.9ambient 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR2.6Bruker software departmentcollection
UXNMR2.6Bruker software departmentprocessing
AURELIA2.7.1Neidig, K.-P., Geyer, M., Goerler, A., Antz, C., Saffrich, R., Beneicke, W. & Kalbitzer, H.Rdata analysis
AUREMOL0.6Ganslmeier, B., Gronwald, W., Ried, A., Neidig, K.-P., Fischer, C. & Kalbitzer, H.R.data analysis
CNS1Bruenger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, Jiang, R.W., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. & Warren, G.L.structure solution
CNS1Bruenger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, Jiang, R.W., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. & Warren, G.L.refinement
RefinementMethod: High temperature torsion angle dynamics. First cooling stage using torsion angle dynamics. Second cooling stage using Cartesian dynamics. Final energy minimization.
Software ordinal: 1
Details: Structures are based on a total of 824 NOE-restraints, 88 backbone dihedral angle restrains, 29 hydrogen bonds and 28 residual dipolar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are the 10 structures with the lowest total energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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