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- PDB-7okw: 1.62A X-ray crystal structure of the conserved C-terminal (CCT) o... -

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Basic information

Entry
Database: PDB / ID: 7okw
Title1.62A X-ray crystal structure of the conserved C-terminal (CCT) of human OSR1
ComponentsSerine/threonine-protein kinase OSR1
KeywordsSIGNALING PROTEIN / KINASE / TRANSFERASE / CCT
Function / homology
Function and homology information


chemokine (C-C motif) ligand 21 signaling pathway / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transport / renal sodium ion absorption / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to chemokine / cellular hyperosmotic response / osmosensory signaling pathway / cell volume homeostasis ...chemokine (C-C motif) ligand 21 signaling pathway / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transport / renal sodium ion absorption / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to chemokine / cellular hyperosmotic response / osmosensory signaling pathway / cell volume homeostasis / peptidyl-threonine phosphorylation / response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / response to xenobiotic stimulus / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / signal transduction / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol
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
Serine/threonine-protein kinase OSR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsBax, B.D. / Elvers, K.T. / 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
DepositionMay 18, 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 / _citation_author.identifier_ORCID / _citation_author.name
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: Serine/threonine-protein kinase OSR1
B: Serine/threonine-protein kinase OSR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9629
Polymers22,5912
Non-polymers3717
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-47 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.168, 49.424, 56.439
Angle α, β, γ (deg.)90.000, 99.442, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-726-

HOH

21A-764-

HOH

31A-784-

HOH

41B-771-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine/threonine-protein kinase OSR1 / Oxidative stress-responsive 1 protein


Mass: 11295.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OXSR1, KIAA1101, OSR1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95747, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 186 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.43 % / Description: plates
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: Morpheus A8: 0.06 M Divalents 0.1 M Buffer System 2 7.5 37.5 % v/v Precipitant Mix 4. Divalents:Mg chloride; Ca chloride. Buffer: pH 7.5 Sodium HEPES; MOPS (acid). Precipitants: 25% v/v MPD; ...Details: Morpheus A8: 0.06 M Divalents 0.1 M Buffer System 2 7.5 37.5 % v/v Precipitant Mix 4. Divalents:Mg chloride; Ca chloride. Buffer: pH 7.5 Sodium HEPES; MOPS (acid). Precipitants: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→55.674 Å / Num. obs: 19062 / % possible obs: 78.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Rrim(I) all: 0.123 / Net I/σ(I): 10
Reflection shellResolution: 1.623→1.764 Å / Num. unique obs: 954 / CC1/2: 0.624 / % possible all: 17.9

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Processing

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

2v3s


Resolution: 1.62→34.61 Å / SU ML: 0.1811 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 930 4.88 %
Rwork0.184 18128 -
obs0.1856 19058 78.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.71 Å2
Refinement stepCycle: LAST / Resolution: 1.62→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 21 179 1648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611570
X-RAY DIFFRACTIONf_angle_d0.87622142
X-RAY DIFFRACTIONf_chiral_restr0.0633254
X-RAY DIFFRACTIONf_plane_restr0.0045290
X-RAY DIFFRACTIONf_dihedral_angle_d12.5366230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.710.2968140.3016360X-RAY DIFFRACTION10.82
1.71-1.820.3081740.25611392X-RAY DIFFRACTION42.88
1.82-1.960.28251610.23993157X-RAY DIFFRACTION95.76
1.96-2.150.21891540.18463295X-RAY DIFFRACTION100
2.15-2.460.20191840.18393264X-RAY DIFFRACTION99.97
2.46-3.10.20921670.19723299X-RAY DIFFRACTION100
3.1-34.610.20791760.16133361X-RAY DIFFRACTION99.89

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