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- PDB-6edx: Crystal Structure of SGK3 PX domain -

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Basic information

Entry
Database: PDB / ID: 6edx
TitleCrystal Structure of SGK3 PX domain
ComponentsSerine/threonine-protein kinase Sgk3
KeywordsTRANSFERASE / PX domain / endosome / trafficking / sorting nexin
Function / homology
Function and homology information


chloride channel regulator activity / regulation of DNA-binding transcription factor activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / calcium channel regulator activity / sodium channel regulator activity / potassium channel regulator activity / regulation of cell migration / phosphatidylinositol binding / regulation of cell growth / recycling endosome ...chloride channel regulator activity / regulation of DNA-binding transcription factor activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / calcium channel regulator activity / sodium channel regulator activity / potassium channel regulator activity / regulation of cell migration / phosphatidylinositol binding / regulation of cell growth / recycling endosome / Stimuli-sensing channels / regulation of cell population proliferation / early endosome / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / cytosol
Similarity search - Function
Serine/threonine-protein kinase Sgk3, catalytic domain / CISK, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Protein kinase, C-terminal ...Serine/threonine-protein kinase Sgk3, catalytic domain / CISK, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase Sgk3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.009 Å
AuthorsChandra, M. / Collins, B.M.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160101743 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1099114 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
CitationJournal: Nat Commun / Year: 2019
Title: Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities.
Authors: Chandra, M. / Chin, Y.K. / Mas, C. / Feathers, J.R. / Paul, B. / Datta, S. / Chen, K.E. / Jia, X. / Yang, Z. / Norwood, S.J. / Mohanty, B. / Bugarcic, A. / Teasdale, R.D. / Henne, W.M. / ...Authors: Chandra, M. / Chin, Y.K. / Mas, C. / Feathers, J.R. / Paul, B. / Datta, S. / Chen, K.E. / Jia, X. / Yang, Z. / Norwood, S.J. / Mohanty, B. / Bugarcic, A. / Teasdale, R.D. / Henne, W.M. / Mobli, M. / Collins, B.M.
History
DepositionAug 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 Sgk3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0882
Polymers13,9961
Non-polymers921
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.339, 74.339, 51.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Serine/threonine-protein kinase Sgk3 / Cytokine-independent survival kinase / Serum/glucocorticoid-regulated kinase 3 / ...Cytokine-independent survival kinase / Serum/glucocorticoid-regulated kinase 3 / Serum/glucocorticoid-regulated kinase-like


Mass: 13996.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SGK3, CISK, SGKL / Production host: Escherichia coli (E. coli)
References: UniProt: Q96BR1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Sodium Citrate, 2M Sodium Malonate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.009→42.59 Å / Num. obs: 9533 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.035 / Net I/σ(I): 13.9
Reflection shellResolution: 2.009→2.06 Å / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 9.1 / Num. unique obs: 682 / CC1/2: 0.99 / Rpim(I) all: 0.051

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTE

1xte


Resolution: 2.009→42.59 Å / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 26.6
RfactorNum. reflection% reflection
Rfree0.2128 966 10.13 %
Rwork0.187 --
obs0.1907 9533 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.009→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 6 21 979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008988
X-RAY DIFFRACTIONf_angle_d0.981328
X-RAY DIFFRACTIONf_dihedral_angle_d15.963381
X-RAY DIFFRACTIONf_chiral_restr0.044134
X-RAY DIFFRACTIONf_plane_restr0.006172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0109-2.11690.26261400.24771193X-RAY DIFFRACTION89
2.1169-2.24940.24661360.25521231X-RAY DIFFRACTION90
2.2494-2.4230.25791340.23331213X-RAY DIFFRACTION90
2.423-2.66660.23611370.23721225X-RAY DIFFRACTION90
2.6666-3.0520.22261360.21451208X-RAY DIFFRACTION90
3.052-3.84320.22741400.16841223X-RAY DIFFRACTION90
3.8432-26.2850.16831430.13371256X-RAY DIFFRACTION90

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