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- PDB-3dae: Crystal structure of phosphorylated SNF1 kinase domain -

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Basic information

Entry
Database: PDB / ID: 3dae
TitleCrystal structure of phosphorylated SNF1 kinase domain
ComponentsCarbon catabolite-derepressing protein kinase
KeywordsTRANSFERASE / kinase / AMPK / snf1 / ATP-binding / Carbohydrate metabolism / Membrane / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


fungal-type cell wall assembly / positive regulation of pseudohyphal growth / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cellular response to glucose starvation / single-species surface biofilm formation / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine shuttle ...fungal-type cell wall assembly / positive regulation of pseudohyphal growth / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cellular response to glucose starvation / single-species surface biofilm formation / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine shuttle / negative regulation of inositol phosphate biosynthetic process / invasive growth in response to glucose limitation / Macroautophagy / AMP-activated protein kinase activity / nucleotide-activated protein kinase complex / filamentous growth / vacuolar membrane / cellular response to stress / nuclear envelope lumen / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / cellular response to glucose starvation / positive regulation of gluconeogenesis / molecular function activator activity / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / nuclear membrane / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / MOLECULAR REPLACEMENT / Resolution: 2.899 Å
AuthorsZheng, L.-S. / Chen, L. / Jiao, Z.-H. / Wu, J.-W.
CitationJournal: Nature / Year: 2009
Title: Structural insight into the autoinhibition mechanism of AMP-activated protein kinase
Authors: Chen, L. / Jiao, Z.-H. / Zheng, L.-S. / Zhang, Y.-Y. / Xie, S.-T. / Wang, Z.-X. / Wu, J.-W.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Carbon catabolite-derepressing protein kinase
B: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)64,8732
Polymers64,8732
Non-polymers00
Water3,369187
1
A: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)32,4371
Polymers32,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)32,4371
Polymers32,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.607, 72.370, 112.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE DEPOSITORS THINK THE SOFTWARE PREDICTED QUATERNARY STRUCTURE IS NOT CONSISTENT WITH BIOCHEMICAL DATA AND MONOMER IS THE BIOLOGICAL UNIT. THE DIMER FORMATION MAY BE DUE TO CRYSTAL PACKING.

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Components

#1: Protein Carbon catabolite-derepressing protein kinase / SNF1


Mass: 32436.666 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residue 41-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNF1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06782, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris pH 8.5, 3.2-3.6M NH4Ac, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.00001 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 24, 2007
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.899→47.2 Å / Num. all: 14122 / Num. obs: 14122 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 50.35 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.7 / Num. measured all: 102012
Reflection shellResolution: 2.899→3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 4.29 / Num. unique all: 1369 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EUE

2eue
PDB Unreleased entry


Resolution: 2.899→47.192 Å / FOM work R set: 0.792 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.265 706 5.01 %random
Rwork0.227 ---
obs0.229 14082 99.9 %-
all-14122 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.136 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 8.63 Å2 / Biso mean: 53.73 Å2 / Biso min: 205.13 Å2
Baniso -1Baniso -2Baniso -3
1-9.182 Å20 Å2-0 Å2
2--6.52 Å20 Å2
3----1.483 Å2
Refinement stepCycle: LAST / Resolution: 2.899→47.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 0 187 4181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134080
X-RAY DIFFRACTIONf_angle_d1.4195512
X-RAY DIFFRACTIONf_chiral_restr0.092619
X-RAY DIFFRACTIONf_plane_restr0.008697
X-RAY DIFFRACTIONf_dihedral_angle_d18.7771516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.898-3.1220.3461490.28525882737
3.122-3.4360.2751390.25326392778
3.436-3.9340.2641420.20426542796
3.934-4.9550.1881320.18226932825
4.955-47.1980.2881440.23828022946

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