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- PDB-6ra0: A ubiquitin-like dimerization domain controls protein kinase D ac... -

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Basic information

Entry
Database: PDB / ID: 6ra0
TitleA ubiquitin-like dimerization domain controls protein kinase D activation by trans-autophosphorylation
ComponentsSerine/threonine-protein kinase dkf-1
KeywordsSIGNALING PROTEIN / ubiquitin-like domain / zinc finger / DAG-binding / C1
Function / homology
Function and homology information


Sphingolipid de novo biosynthesis / activation of immune response / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / neuromuscular synaptic transmission / determination of adult lifespan / positive regulation of protein import into nucleus / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / intracellular signal transduction ...Sphingolipid de novo biosynthesis / activation of immune response / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / neuromuscular synaptic transmission / determination of adult lifespan / positive regulation of protein import into nucleus / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / intracellular signal transduction / defense response to Gram-positive bacterium / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / synapse / positive regulation of gene expression / ATP binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Serine/threonine-protein kinase, active site ...Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase dkf-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsElsner, D.J. / Leonard, T.A.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP28135 Austria
Austrian Science FundP30584 Austria
CitationJournal: J.Biol.Chem. / Year: 2019
Title: A ubiquitin-like domain controls protein kinase D dimerization and activation by trans-autophosphorylation.
Authors: Elsner, D.J. / Siess, K.M. / Gossenreiter, T. / Hartl, M. / Leonard, T.A.
History
DepositionApr 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 dkf-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2873
Polymers17,1571
Non-polymers1312
Water00
1
A: Serine/threonine-protein kinase dkf-1
hetero molecules

A: Serine/threonine-protein kinase dkf-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5756
Polymers34,3132
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)45.413, 83.018, 37.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Serine/threonine-protein kinase dkf-1


Mass: 17156.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: dkf-1, W09C5.5 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): STAR / References: UniProt: Q9XUJ7, protein kinase C
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 6.8% PEG8000 18% ethylene glycol 0.1 M MES, pH 6.5 0.03 M NaF 0.03 M NaBr 0.03 M NaI

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.97626
SYNCHROTRONESRF ID2921.28254
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELJun 21, 2015
DECTRIS PILATUS 6M-F2PIXELJun 21, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.976261
21.282541
ReflectionResolution: 2.26→50 Å / Num. obs: 6939 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 57.34 Å2 / Net I/σ(I): 11.2
Reflection shellResolution: 2.26→2.38 Å / Num. unique obs: 641

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→41.51 Å / SU ML: 0.304 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.6171
RfactorNum. reflection% reflection
Rfree0.2762 350 5.07 %
Rwork0.2317 --
obs0.2339 6910 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 72.71 Å2
Refinement stepCycle: LAST / Resolution: 2.26→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 2 0 1097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871115
X-RAY DIFFRACTIONf_angle_d1.07081503
X-RAY DIFFRACTIONf_chiral_restr0.0617165
X-RAY DIFFRACTIONf_plane_restr0.0051198
X-RAY DIFFRACTIONf_dihedral_angle_d4.5351680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.590.37871080.31752116X-RAY DIFFRACTION98.76
2.59-3.260.36791290.30592160X-RAY DIFFRACTION99.35
3.26-41.520.23651130.20112284X-RAY DIFFRACTION99.63
Refinement TLS params.Method: refined / Origin x: 34.5467500026 Å / Origin y: 9.74707700077 Å / Origin z: -5.52593846825 Å
111213212223313233
T0.481015541219 Å20.0648093085188 Å20.0279585604037 Å2-0.500713396558 Å2-0.0112260742284 Å2--0.581513945844 Å2
L1.48582795069 °2-0.799773042442 °20.707191284895 °2-4.26394444438 °2-1.12041184521 °2--2.0374996774 °2
S0.141111713507 Å °0.0268571595094 Å °-0.208242585252 Å °-0.196061025667 Å °-0.0954576663593 Å °0.382624591759 Å °-0.241715544491 Å °-0.254065239378 Å °-0.0277004875458 Å °
Refinement TLS groupSelection details: all

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