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- PDB-1q97: The structure of the Saccharomyces cerevisiae SR protein kinase, ... -

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Basic information

Entry
Database: PDB / ID: 1q97
TitleThe structure of the Saccharomyces cerevisiae SR protein kinase, Sky1p, with bound ATP
ComponentsSR protein kinase
KeywordsTRANSFERASE / protein 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 / cytoplasmic stress granule / positive regulation of protein import into nucleus / 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 / cytoplasmic stress granule / positive regulation of protein import into nucleus / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
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. ...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
ADENOSINE / ADENOSINE-5'-TRIPHOSPHATE / NICKEL (II) ION / Serine/threonine-protein kinase SKY1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)87,1249
Polymers86,0502
Non-polymers1,0747
Water2,612145
1
A: SR protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6775
Polymers43,0251
Non-polymers6524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SR protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4474
Polymers43,0251
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.823, 88.692, 133.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SR protein kinase


Mass: 43025.066 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 152 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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, VAPOR DIFFUSION, HANGING DROP, 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: 2.3→48.89 Å / Num. all: 38590 / Num. obs: 33170 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.5 Å2 / Limit h max: 31 / Limit h min: 0 / Limit k max: 37 / Limit k min: 0 / Limit l max: 57 / Limit l min: 0 / Observed criterion F max: 386807.55 / Observed criterion F min: 1.049
Reflection shellResolution: 2.3→2.38 Å / % possible all: 83.3
Reflection
*PLUS
Num. measured all: 178325 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 83.3 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
XTALVIEWrefinement
RefinementResolution: 2.3→19.89 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1548 5 %RANDOM
Rwork0.215 ---
all-38590 --
obs-33170 86 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 41.1739 Å2 / ksol: 0.394757 e/Å3
Displacement parametersBiso max: 89.3 Å2 / Biso mean: 35.84 Å2 / Biso min: 10.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.3 Å20 Å20 Å2
2---9.64 Å20 Å2
3---6.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5732 0 63 145 5940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg22.2
X-RAY DIFFRACTIONc_torsion_impr_deg0.76
LS refinement shellResolution: 2.3→2.41 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.314 175 5.1 %
Rwork0.256 3242 -
all-4763 -
obs-3417 83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ligand_5.paramligand_5.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 29551 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2563 / Rfactor Rwork: 0.2039
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.27

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