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- PDB-1how: THE X-RAY CRYSTAL STRUCTURE OF SKY1P, AN SR PROTEIN KINASE IN YEAST -

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Basic information

Entry
Database: PDB / ID: 1how
TitleTHE X-RAY CRYSTAL STRUCTURE OF SKY1P, AN SR PROTEIN KINASE IN YEAST
ComponentsSERINE/THREONINE-PROTEIN KINASE YMR216C
KeywordsTRANSFERASE / KINASE
Function / homology
Function and homology information


intracellular monoatomic cation homeostasis / intracellular monoatomic ion homeostasis / regulation of mRNA processing / mRNA splice site recognition / stress granule disassembly / regulation of cell size / spliceosomal complex assembly / positive regulation of protein import into nucleus / cytoplasmic stress granule / non-specific serine/threonine protein kinase ...intracellular monoatomic cation homeostasis / intracellular monoatomic ion homeostasis / regulation of mRNA processing / mRNA splice site recognition / stress granule disassembly / regulation of cell size / spliceosomal complex assembly / positive regulation of protein import into nucleus / cytoplasmic stress granule / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / 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 ...: / 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
Serine/threonine-protein kinase SKY1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsNolen, B.J. / Yun, C.Y. / Wong, C.F. / McCammon, J.A. / Fu, X.-D. / Ghosh, G.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The structure of Sky1p reveals a novel mechanism for constitutive activity.
Authors: Nolen, B. / Yun, C.Y. / Wong, C.F. / McCammon, J.A. / Fu, X.D. / Ghosh, G.
History
DepositionDec 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE YMR216C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7109
Polymers43,0091
Non-polymers7018
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.403, 88.322, 135.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE YMR216C


Mass: 43009.066 Da / Num. of mol.: 1 / Fragment: SKY1PDELTANS
Mutation: 137 A.A. TRUNCATED FROM N-TERMINUS, RESIDUES 305-542 REMOVED AND REPLACED WITH VDSQK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YMR216C / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q03656, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Ammonium Sulfate, Ethylene Glycol, Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.0066 mMATP1drop
30.0017 mM1dropMg2+
41.5 Mammonium sulfate1reservoir
515 %(v/v)ethylene glycol1reservoir
610 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 8, 1999 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 29021 / Num. obs: 24675 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.6
Reflection shellResolution: 2.1→2.19 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3.3 / % possible all: 91.8
Reflection
*PLUS
Num. measured all: 235953
Reflection shell
*PLUS
% possible obs: 91.8 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: RESIDUES MENTIONED IN REMARK 470 WERE MODELED AS ALA DUE TO POOR ELECTRON DENSITY
RfactorNum. reflectionSelection details
Rfree0.255 992 RANDOM
Rwork0.204 --
all-26167 -
obs-20490 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 38 204 3004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_bond_d0.0053
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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