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- PDB-1q99: Crystal structure of the Saccharomyces cerevisiae SR protein kins... -

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Basic information

Entry
Database: PDB / ID: 1q99
TitleCrystal structure of the Saccharomyces cerevisiae SR protein kinsae, Sky1p, complexed with the non-hydrolyzable ATP analogue, AMP-PNP
ComponentsSR protein kinsae
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / METHANOL / NICKEL (II) ION / Serine/threonine-protein kinase SKY1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.11 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_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_conn_type.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 kinsae
B: SR protein kinsae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,56012
Polymers86,0502
Non-polymers1,51010
Water4,288238
1
A: SR protein kinsae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7806
Polymers43,0251
Non-polymers7555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SR protein kinsae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7806
Polymers43,0251
Non-polymers7555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.413, 88.947, 134.822
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 kinsae


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, 248 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MOH / METHANOL / Methanol


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


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.5 M (NH4)2SO4, 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

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.54 Å
DetectorType: SBC-2 / Detector: CCD / Date: Nov 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.11→40.11 Å / Num. all: 51095 / Num. obs: 49258 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.7 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 42 / Limit k min: 0 / Limit l max: 63 / Limit l min: 0 / Observed criterion F max: 330018.77 / Observed criterion F min: 1.049
Reflection shellResolution: 2.11→2.18 Å / % possible all: 86.6
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 49644 / % possible obs: 96.5 % / Num. measured all: 280589 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
Rmerge(I) obs: 46.7 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SORTRFdata scaling
XTALVIEWrefinement
RefinementResolution: 2.11→19.95 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2342 5 %random
Rwork0.22 ---
all-51095 --
obs-49258 96.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 53.0035 Å2 / ksol: 0.39012 e/Å3
Displacement parametersBiso max: 81.86 Å2 / Biso mean: 31.8 Å2 / Biso min: 7.81 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å20 Å2
2---1.08 Å20 Å2
3----2.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Luzzati d res high-2.1
Refinement stepCycle: LAST / Resolution: 2.11→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5788 0 82 242 6112
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg21.8
X-RAY DIFFRACTIONc_torsion_impr_deg0.81
LS refinement shellResolution: 2.11→2.2 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.331 268 5.5 %
Rwork0.302 4570 -
all-6319 -
obs-4838 86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ligand_3.paramligand_3.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Num. reflection obs: 41455 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2601 / Rfactor Rwork: 0.2201
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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