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- PDB-1q8z: The apoenzyme structure of the yeast SR protein kinase, Sky1p -

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Basic information

Entry
Database: PDB / ID: 1q8z
TitleThe apoenzyme structure of the yeast SR protein kinase, Sky1p
ComponentsSR Protein Kinase
KeywordsTRANSFERASE / disallowed / 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 / protein kinase activity ...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 / protein kinase activity / non-specific serine/threonine protein kinase / 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
METHANOL / Serine/threonine-protein kinase SKY1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsNolen, B. / Ngo, J. / Chakrabarti, S. / Vu, D. / Adams, J.A. / Ghosh, G.
CitationJournal: Biochemistry / Year: 2003
Title: Nucleotide-Induced Conformational Changes in the Saccharomyces cerevisiae SR Protein Kinase, Sky1p, Revealed by X-Ray Crystallography
Authors: Nolen, B. / Ngo, J. / Chakrabarti, S. / Vu, D. / Adams, J.A. / Ghosh, G.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE 137 amino acids truncated from N-terminus, RESIDUES 305-538 WERE DELETED AND REPLACED WITH VAL-ASP

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SR Protein Kinase
B: SR Protein Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4308
Polymers86,0502
Non-polymers3806
Water2,396133
1
A: SR Protein Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2154
Polymers43,0251
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SR Protein Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2154
Polymers43,0251
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.990, 88.701, 135.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SR Protein Kinase


Mass: 43025.066 Da / Num. of mol.: 2 / Fragment: Sky1pdeltaN(137)deltaS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKY1 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLyS
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.: 2 / 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: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 298 K / pH: 4.5
Details: 1.5M (NH4)2SO4, 100mM Na Acetate pH 4.5, 15% Ethylene Glycol. Crystals then dialyzed into 30% PEG 400 and 100mM Na Acetate pH 4.5, hanging drop, crystals soaked into low salt buffer, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Nolen, B., (2001) Nat.Struct.Biol., 8, 176.
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: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.54 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 37306 / Num. obs: 34172 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067 / Net I/σ(I): 10.3
Reflection shellResolution: 2.35→2.43 Å / % possible all: 85.6
Reflection
*PLUS
Num. measured all: 198041 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 85.6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.39

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
XTALVIEWrefinement
HKL-2000data collection
HKL-2000data reduction
RefinementStarting model: PDB code 1HOW

1how


Resolution: 2.35→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.259 1424 -
Rwork0.221 --
all-37319 -
obs-34172 91.6 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.814 Å20 Å20 Å2
2--5.444 Å20 Å2
3---5.37 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5788 0 18 137 5943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3241.5
X-RAY DIFFRACTIONc_mcangle_it2.2242
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.8692.5
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.33
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2moh_edo.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
Refinement
*PLUS
Num. reflection obs: 28641 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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