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- PDB-5o1v: Crystal structure of WNK3 kinase domain in a monophosphorylated a... -

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Basic information

Entry
Database: PDB / ID: 5o1v
TitleCrystal structure of WNK3 kinase domain in a monophosphorylated apo state (A-loop swapped)
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 / non-membrane-bounded organelle assembly / regulation of calcium ion import / osmosensory signaling pathway / positive regulation of sodium ion transport / 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 / non-membrane-bounded organelle assembly / regulation of calcium ion import / osmosensory signaling pathway / positive regulation of sodium ion transport / cellular hyperosmotic response / positive regulation of calcium ion transport / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / maintenance of blood-brain barrier / bicellular tight junction / molecular condensate scaffold activity / positive regulation of peptidyl-threonine phosphorylation / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / adherens junction / peptidyl-threonine phosphorylation / 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 kinases, catalytic 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: 1.723 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Kupinska, K. / Wang, D. / Fairhead, M. / Kopec, J. / Sethi, R. / Dixon-Clarke, S.E. / Chalk, R. / Berridge, G. ...Pinkas, D.M. / Bufton, J.C. / Kupinska, K. / Wang, D. / Fairhead, M. / Kopec, J. / Sethi, R. / Dixon-Clarke, S.E. / 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 apo state (A-loop swapped)
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

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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)66,46318
Polymers65,4702
Non-polymers99316
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint17 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.966, 67.484, 79.895
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number4
Space group name H-MP1211

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG4000, 10% 2-propanol, 0.1M HEPES pH 7.5. 2:1 protein to reservoir.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.72→67.48 Å / Num. obs: 56586 / % possible obs: 85.6 % / Redundancy: 3.3 % / Net I/σ(I): 18.1

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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: 1.723→51.486 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.66
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 2685 4.75 %Random Selection
Rwork0.1729 ---
obs0.1746 56552 85.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.723→51.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 64 432 4844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054518
X-RAY DIFFRACTIONf_angle_d0.6866071
X-RAY DIFFRACTIONf_dihedral_angle_d15.7212731
X-RAY DIFFRACTIONf_chiral_restr0.052671
X-RAY DIFFRACTIONf_plane_restr0.005765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7234-1.75470.36441350.31012971X-RAY DIFFRACTION91
1.7547-1.78850.32791810.27143270X-RAY DIFFRACTION100
1.7885-1.8250.29621450.24943338X-RAY DIFFRACTION100
1.825-1.86470.28381520.22263309X-RAY DIFFRACTION100
1.8647-1.90810.2536650.23181230X-RAY DIFFRACTION41
1.9081-1.95580.28921060.21452070X-RAY DIFFRACTION91
1.9558-2.00870.28451650.20893268X-RAY DIFFRACTION100
2.0087-2.06780.2601990.20441730X-RAY DIFFRACTION93
2.0678-2.13450.2635570.19151182X-RAY DIFFRACTION91
2.1345-2.21080.22421460.1833308X-RAY DIFFRACTION100
2.2108-2.29930.23611480.17662902X-RAY DIFFRACTION88
2.2993-2.4040.22011760.17363282X-RAY DIFFRACTION100
2.404-2.53070.24661600.18493312X-RAY DIFFRACTION100
2.5307-2.68930.24831350.18222623X-RAY DIFFRACTION79
2.6893-2.89690.20551610.17453321X-RAY DIFFRACTION100
2.8969-3.18840.19511530.18083299X-RAY DIFFRACTION99
3.1884-3.64960.19291630.16123068X-RAY DIFFRACTION92
3.6496-4.59770.17661650.13723039X-RAY DIFFRACTION94
4.5977-51.50920.1731730.16313345X-RAY DIFFRACTION98

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