- PDB-1z1v: NMR structure of the Saccharomyces cerevisiae Ste50 SAM domain -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1z1v
Title
NMR structure of the Saccharomyces cerevisiae Ste50 SAM domain
Components
STE50 protein
Keywords
CELL CYCLE / all helix protein / SAM domain
Function / homology
Function and homology information
osmosensory signaling pathway via Sho1 osmosensor / signal transduction involved in filamentous growth / SAM domain binding / pheromone-dependent signal transduction involved in conjugation with cellular fusion / protein kinase regulator activity / p38MAPK cascade / regulation of cell cycle / cell cycle / cytoplasm Similarity search - Function
Mass: 9309.657 Da / Num. of mol.: 1 / Fragment: ste50 SAM domain (residues 32-107) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Description: this protein fragment was cloned into the NdeI and BamHI sites of pET15b creating an aminoterminal hexahistidine tagged protein with an intervening thrombin protease cleavage site. After ...Description: this protein fragment was cloned into the NdeI and BamHI sites of pET15b creating an aminoterminal hexahistidine tagged protein with an intervening thrombin protease cleavage site. After thrombin treatment, the non-native residues GSH remained amino terminal to the native Ste50 sequence Gene: STE50 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25344
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 13C-separated NOESY
1
2
1
3D 15N-separated NOESY
NMR details
Text: This structure was determined using standard 3D heteronuclear techniques
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Sample preparation
Details
Contents: 0.8 mM Ste50 SAM U-15N,13C, 20 mM sodium phosphate buffer, pH 7.8, 150 mM sodium chloride, 0.02 % sodium azide, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O
Sample conditions
Ionic strength: 150 mM NaCl / pH: 7.8 / Pressure: 1 atm / Temperature: 293 K
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE
Bruker
AVANCE
600
1
Varian INOVA
Varian
INOVA
800
2
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Processing
NMR software
Name
Version
Developer
Classification
NMRPipe
Delagio
processing
NMRView
5.2
Johnson
dataanalysis
CYANA
2
Guntert
structuresolution
XPLOR-NIH
2.9.9
refinement
Refinement
Method: simulated annealing / Software ordinal: 1 Details: Experimental observations: 615 intermolecular NOE distance restraints, 328 short range NOE distance restraints, 163 medium range NOE distance restraints, 149 long range NOE restraints, 42 ...Details: Experimental observations: 615 intermolecular NOE distance restraints, 328 short range NOE distance restraints, 163 medium range NOE distance restraints, 149 long range NOE restraints, 42 pairs of hydrogen bond distance restraints and 69 pairs of phi/psi dihedral angle restraints. An initial ensemble of 500 structures were calculated with CYANA 2.0. The top 25 structures with minimum restraint violations were refined in water using XPLOR-NIH and a protocol by C. Spronk. All 25 water refined structures had no NOE violations > 0.5 A and no dihedral violations > 5 degrees. For residues 35-100, the backbone RMSD of the ensemble is 0.75 +/- 0.14 A. Residues 28-32 and 101-107 are disordered.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformers submitted total number: 1
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