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- PDB-7o86: 1.73A X-ray crystal structure of the conserved C-terminal (CCT) o... -

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Basic information

Entry
Database: PDB / ID: 7o86
Title1.73A X-ray crystal structure of the conserved C-terminal (CCT) of human SPAK
ComponentsSTE20/SPS1-related proline-alanine-rich protein kinase
KeywordsSIGNALING PROTEIN / KINASE / TRANSFERASE / CCT
Function / homology
Function and homology information


negative regulation of creatine transmembrane transporter activity / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / maintenance of lens transparency / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of sodium ion transmembrane transporter activity / renal sodium ion absorption ...negative regulation of creatine transmembrane transporter activity / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / maintenance of lens transparency / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of sodium ion transmembrane transporter activity / renal sodium ion absorption / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to potassium ion / macrophage activation / positive regulation of potassium ion transport / cellular response to chemokine / cellular hyperosmotic response / cell volume homeostasis / positive regulation of p38MAPK cascade / response to aldosterone / response to dietary excess / sodium ion transmembrane transport / peptidyl-threonine phosphorylation / regulation of blood pressure / kinase activity / cell cortex / regulation of inflammatory response / cell body / peptidyl-serine phosphorylation / basolateral plasma membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / inflammatory response / apical plasma membrane / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / signal transduction / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / : / 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
Similarity search - Domain/homology
STE20/SPS1-related proline-alanine-rich protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsElvers, K.T. / Bax, B.D. / Lipka-Lloyd, M. / Mehellou, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)518455 United Kingdom
CitationJournal: Chembiochem / Year: 2022
Title: Structures of the Human SPAK and OSR1 Conserved C-Terminal (CCT) Domains.
Authors: Elvers, K.T. / Lipka-Lloyd, M. / Trueman, R.C. / Bax, B.D. / Mehellou, Y.
History
DepositionApr 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 19, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STE20/SPS1-related proline-alanine-rich protein kinase
B: STE20/SPS1-related proline-alanine-rich protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0706
Polymers22,9602
Non-polymers1104
Water3,675204
1
A: STE20/SPS1-related proline-alanine-rich protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5263
Polymers11,4801
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STE20/SPS1-related proline-alanine-rich protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5443
Polymers11,4801
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.611, 50.549, 103.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein STE20/SPS1-related proline-alanine-rich protein kinase / Ste-20-related kinase / DCHT / Serine/threonine-protein kinase 39


Mass: 11479.870 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK39, SPAK / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UEW8, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 150nls Protein (1.4mgs/ml in 20 mM Tris.HCl pH 7.8, 50mM NaCl, 1mM DTT) was mixed with 50nl Morpheus A5 = 30mM Magnesium chloride hexahydrate, 30mM Calcium chloride dihydrate, 50mM Sodium ...Details: 150nls Protein (1.4mgs/ml in 20 mM Tris.HCl pH 7.8, 50mM NaCl, 1mM DTT) was mixed with 50nl Morpheus A5 = 30mM Magnesium chloride hexahydrate, 30mM Calcium chloride dihydrate, 50mM Sodium HEPES, 50mM MOPS pH 7.5, 20% v/v PEG 500* MME, 10% w/v PEG 20000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.73→45.45 Å / Num. obs: 22482 / % possible obs: 99.63 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.82 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.07308 / Rrim(I) all: 0.2657 / Net I/σ(I): 6.83
Reflection shellResolution: 1.73→1.792 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 0.43 / Num. unique obs: 2168 / CC1/2: 0.281 / CC star: 0.663 / % possible all: 97.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v3s

2v3s


Resolution: 1.73→45.45 Å / SU ML: 0.3087 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.2007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 1100 4.91 %
Rwork0.1988 21308 -
obs0.2009 22408 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.62 Å2
Refinement stepCycle: LAST / Resolution: 1.73→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 4 204 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01231751
X-RAY DIFFRACTIONf_angle_d1.17172408
X-RAY DIFFRACTIONf_chiral_restr0.0834277
X-RAY DIFFRACTIONf_plane_restr0.006338
X-RAY DIFFRACTIONf_dihedral_angle_d18.0473667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.810.37951470.3742561X-RAY DIFFRACTION98.12
1.81-1.90.37511300.31942620X-RAY DIFFRACTION99.78
1.9-2.020.30771350.26852625X-RAY DIFFRACTION99.6
2.02-2.180.28411170.21572663X-RAY DIFFRACTION99.78
2.18-2.40.22641370.18912633X-RAY DIFFRACTION99.89
2.4-2.750.25431400.1922666X-RAY DIFFRACTION99.82
2.75-3.460.26871370.17692706X-RAY DIFFRACTION100
3.46-45.450.18081570.17022834X-RAY DIFFRACTION99.93

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