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- PDB-5o21: Crystal structure of WNK3 kinase domain in a monophosphorylated s... -

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Basic information

Entry
Database: PDB / ID: 5o21
TitleCrystal structure of WNK3 kinase domain in a monophosphorylated state with chloride bound in the active site
ComponentsSerine/threonine-protein kinase WNK3
KeywordsSTRUCTURAL GENOMICS / WNK3 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / regulation of calcium ion import / osmosensory signaling pathway / positive regulation of sodium ion transport / membraneless organelle assembly / cellular hyperosmotic response / positive regulation of calcium ion transport ...positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / regulation of calcium ion import / osmosensory signaling pathway / positive regulation of sodium ion transport / membraneless organelle assembly / cellular hyperosmotic response / positive regulation of calcium ion transport / cell volume homeostasis / regulation of monoatomic cation transmembrane transport / maintenance of blood-brain barrier / bicellular tight junction / negative regulation of protein localization to plasma membrane / positive regulation of peptidyl-threonine phosphorylation / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / adherens junction / peptidyl-threonine phosphorylation / molecular condensate scaffold activity / Stimuli-sensing channels / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
: / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / 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 kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / 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 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 WNK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Kupinska, K. / Wang, D. / Fairhead, M. / Chalk, R. / Berridge, G. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. ...Pinkas, D.M. / Bufton, J.C. / Kupinska, K. / Wang, D. / Fairhead, M. / Chalk, R. / Berridge, G. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of WNK3 kinase domain in a monophosphorylated state with chloride bound in the active site
Authors: Pinkas, D.M. / Daubner, G.M. / Bufton, J.C. / Bartual, S.G. / Sanvitale, C.E. / Alessi, D.R. / Bullock, A.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK3
B: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,53420
Polymers65,4702
Non-polymers1,06418
Water6,666370
1
A: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,26710
Polymers32,7351
Non-polymers5329
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,26710
Polymers32,7351
Non-polymers5329
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.410, 117.410, 46.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Serine/threonine-protein kinase WNK3 / Protein kinase lysine-deficient 3 / Protein kinase with no lysine 3


Mass: 32734.852 Da / Num. of mol.: 2 / Fragment: UNP residues 132-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK3, KIAA1566, PRKWNK3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYP7, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 22.5% PEG Smear Broad, 0.1 M sodium/potassium tartrate, 10% ethylene glycol, 0.1 M cacodylate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.77 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.06→58.71 Å / Num. obs: 43853 / % possible obs: 99.9 % / Redundancy: 32.7 % / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→58.705 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.87
RfactorNum. reflection% reflection
Rfree0.2209 2292 5.23 %
Rwork0.1799 --
obs0.182 43830 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→58.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 66 370 4836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024540
X-RAY DIFFRACTIONf_angle_d0.5146082
X-RAY DIFFRACTIONf_dihedral_angle_d15.8512756
X-RAY DIFFRACTIONf_chiral_restr0.043667
X-RAY DIFFRACTIONf_plane_restr0.003759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.10480.35511800.28682589X-RAY DIFFRACTION100
2.1048-2.15380.33341370.27432545X-RAY DIFFRACTION100
2.1538-2.20760.32591300.24632654X-RAY DIFFRACTION100
2.2076-2.26730.2421610.23242543X-RAY DIFFRACTION100
2.2673-2.3340.2541140.21172637X-RAY DIFFRACTION100
2.334-2.40940.24371940.19252551X-RAY DIFFRACTION100
2.4094-2.49550.2581170.1982593X-RAY DIFFRACTION100
2.4955-2.59540.25961460.19782628X-RAY DIFFRACTION100
2.5954-2.71350.22841440.19682589X-RAY DIFFRACTION100
2.7135-2.85660.27451440.18982606X-RAY DIFFRACTION100
2.8566-3.03560.23451830.18552545X-RAY DIFFRACTION100
3.0356-3.26990.21681260.18262624X-RAY DIFFRACTION100
3.2699-3.59890.19691290.16762598X-RAY DIFFRACTION100
3.5989-4.11960.1758980.15362639X-RAY DIFFRACTION100
4.1196-5.18980.16251560.1462591X-RAY DIFFRACTION100
5.1898-58.72880.22341330.16922606X-RAY DIFFRACTION100

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