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- PDB-2fh9: Structure and dimerization of the kinase domain from yeast Snf1 -

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Basic information

Entry
Database: PDB / ID: 2fh9
TitleStructure and dimerization of the kinase domain from yeast Snf1
ComponentsSnf1 kinase
KeywordsSIGNALING PROTEIN / TRANSFERASE / kinase domain / dimer
Function / homology
Function and homology information


fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism ...fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism / invasive growth in response to glucose limitation / Macroautophagy / filamentous growth / nucleotide-activated protein kinase complex / vacuolar membrane / AMP-activated protein kinase activity / nuclear envelope lumen / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / molecular function activator activity / nuclear membrane / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Carbon catabolite-derepressing protein kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsNayak, V.
CitationJournal: Structure / Year: 2006
Title: Structure and Dimerization of the Kinase Domain from Yeast Snf1, a Member of the Snf1/AMPK Protein Family
Authors: Nayak, V. / Zhao, K. / Wyce, A. / Schwartz, M.F. / Lo, W.S. / Berger, S.L. / Marmorstein, R.
History
DepositionDec 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Snf1 kinase


Theoretical massNumber of molelcules
Total (without water)31,2551
Polymers31,2551
Non-polymers00
Water1,892105
1
A: Snf1 kinase

A: Snf1 kinase


Theoretical massNumber of molelcules
Total (without water)62,5112
Polymers62,5112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3100 Å2
ΔGint-20 kcal/mol
Surface area24150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.677, 108.677, 61.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-354-

HOH

31A-357-

HOH

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Components

#1: Protein Snf1 kinase / E.C.2.7.1.- / Carbon catabolite derepressing protein kinase


Mass: 31255.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNF1, CAT1, CCR1, GLC2, PAS14 / Plasmid: pRSET 1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P06782, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.2M magnesium chloride, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9686, 0.9796, 0.9794
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97961
30.97941
Reflection
IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)% possible obs
177740.1031.788350100
277880.1011.101350100
3140800.0861.065350100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.465099.910.0574.739
5.136.4699.910.0983.369
4.485.1310010.0732.109
4.074.4810010.0741.597
3.784.0710010.0881.33
3.563.7810010.1241.117
3.383.5610010.1821.016
3.233.3810010.2580.898
3.113.2310010.3620.914
33.1110010.4850.919
6.465099.920.0361.524
5.136.4699.920.0871.848
4.485.1310020.0621.163
4.074.4810020.0691.012
3.784.0710020.0910.978
3.563.7810020.1420.943
3.383.5610020.2130.899
3.233.3810020.3160.856
3.113.2310020.4650.893
33.1110020.6330.917
6.465099.930.0270.788
5.136.4699.930.0781.839
4.485.1310030.0571.196
4.074.4810030.0641.144
3.784.0710030.0831.119
3.563.7810030.1251.049
3.383.5610030.1790.965
3.233.3810030.2570.868
3.113.2310030.3730.845
33.1110030.4990.866
ReflectionResolution: 2.8→50 Å / Num. all: 9543 / Num. obs: 8763 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 3 Å / D res low: 20 Å / FOM : 0.63 / Reflection: 7573
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.96863.31-4.99
13 wavelength20.97962.37-9.88
13 wavelength30.97945.1-8.02
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se57.6160.0740.3750.2451.038
2Se52.7430.1430.2510.2621.114
3Se45.6740.1750.3450.220.941
4Se600.130.2020.2180.953
5Se600.3160.0560.3280.967
Phasing MAD shell
Resolution (Å)FOM Reflection
9.92-200.83452
6.57-9.920.85670
5.23-6.570.83816
4.47-5.230.8945
3.96-4.470.731051
3.6-3.960.581149
3.32-3.60.441192
3.1-3.320.311298
Phasing dmFOM : 0.7 / FOM acentric: 0.71 / FOM centric: 0.67 / Reflection: 7583 / Reflection acentric: 6212 / Reflection centric: 1371
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-19.9630.950.970.93354207147
5.4-8.60.90.920.851069789280
4.3-5.40.890.910.8112991049250
3.8-4.30.810.840.712791064215
3.2-3.80.590.610.4822221916306
3-3.20.360.380.2213601187173

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.02phasing
RESOLVE2.02phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 897 9.4 %random
Rwork0.215 ---
all0.345 9543 --
obs0.336 8763 91.8 %-
Solvent computationBsol: 37.864 Å2
Displacement parametersBiso mean: 52.132 Å2
Baniso -1Baniso -2Baniso -3
1--2.718 Å20 Å20 Å2
2---2.718 Å20 Å2
3---5.436 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 0 105 2162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007225
X-RAY DIFFRACTIONc_angle_deg1.38321
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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