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- PDB-1ow5: NMR structure of the Saccharomyces cerevisiae SAM (Sterile Alpha ... -

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Basic information

Entry
Database: PDB / ID: 1ow5
TitleNMR structure of the Saccharomyces cerevisiae SAM (Sterile Alpha Motif) domain
ComponentsSerine/threonine-protein kinase STE11
KeywordsTRANSFERASE / MAP kinase / MAPKKK / SAM domain / Pointed domain / SCM domain / Ste50 regulator
Function / homology
Function and homology information


cell integrity MAPK cascade / osmosensory signaling pathway via Sho1 osmosensor / signal transduction involved in filamentous growth / pheromone response MAPK cascade / SAM domain binding / pseudohyphal growth / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / mitogen-activated protein kinase kinase kinase / Oxidative Stress Induced Senescence ...cell integrity MAPK cascade / osmosensory signaling pathway via Sho1 osmosensor / signal transduction involved in filamentous growth / pheromone response MAPK cascade / SAM domain binding / pseudohyphal growth / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / mitogen-activated protein kinase kinase kinase / Oxidative Stress Induced Senescence / p38MAPK cascade / MAP kinase kinase kinase activity / protein kinase activity / phosphorylation / protein serine kinase activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 ...Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase STE11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing from an extended starting structure
AuthorsDonaldson, L.W.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The solution structure of the S.cerevisiae Ste11 MAPKKK SAM domain and its partnership with Ste50.
Authors: Kwan, J.J. / Warner, N. / Pawson, T. / Donaldson, L.W.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: Serine/threonine-protein kinase STE11


Theoretical massNumber of molelcules
Total (without water)10,0451
Polymers10,0451
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)1 / 500structures with acceptable covalent geometry
RepresentativeModel #1no violations > 0.5 a, lowest energy, good geometry

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Components

#1: Protein Serine/threonine-protein kinase STE11 / Ste11 MAPKKK SAM domain


Mass: 10045.456 Da / Num. of mol.: 1 / Fragment: SAM domain (residues 36-113)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Ste11p / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P23561, 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
11113C/15N simultaneous 3D NOESY
1212D NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques. Assignments were derived from HNCACB, CBCACONH, CBHD, CBHE, HCCH-TOCSY, HCC-TOCSY and CCC-TOCSY experiments

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Sample preparation

DetailsContents: 0.8 mM Ste11 SAM domain, U-15N,13C
Solvent system: 20 mM sodium phosphate buffer, 500 mM sodium chloride, 0.03% sodium azide, 90% H2O, 10% D2O
Sample conditionsIonic strength: 500 mM sodium chloride / pH: 6.8 / 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
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglioprocessing
X-PLORNIHBrunger, Clorestructure solution
NMRView5Johnsondata analysis
X-PLORNIHBrunger, Clorerefinement
RefinementMethod: simulated annealing from an extended starting structure
Software ordinal: 1
Details: 971 NOE restraints from a simultaneous 13C/15N NOESY in 10% D2O, 69 NOE restraints from a 2D NOESY in 99% D2O, 48 hydrogen bonds restraints and 59 pairs of phi/psi dihedral restraints from ...Details: 971 NOE restraints from a simultaneous 13C/15N NOESY in 10% D2O, 69 NOE restraints from a 2D NOESY in 99% D2O, 48 hydrogen bonds restraints and 59 pairs of phi/psi dihedral restraints from chemical shifts using the TALOS method
NMR representativeSelection criteria: no violations > 0.5 a, lowest energy, good geometry
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 500 / Conformers submitted total number: 1

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