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- PDB-5ve6: Crystal structure of Sugen kinase 223 -

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Basic information

Entry
Database: PDB / ID: 5ve6
TitleCrystal structure of Sugen kinase 223
ComponentsTyrosine-protein kinase SgK223
KeywordsSIGNALING PROTEIN / kinase / pseudokinase
Function / homology
Function and homology information


regulation of Notch signaling pathway / regulation of cell motility / positive regulation of Rho protein signal transduction / cell migration / negative regulation of neuron projection development / regulation of cell shape / protein kinase activity / protein phosphorylation / focal adhesion / identical protein binding ...regulation of Notch signaling pathway / regulation of cell motility / positive regulation of Rho protein signal transduction / cell migration / negative regulation of neuron projection development / regulation of cell shape / protein kinase activity / protein phosphorylation / focal adhesion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Inactive tyrosine-protein kinase PRAG1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.953 Å
AuthorsPatel, O. / Lucet, I. / Panjikar, S.
CitationJournal: Nat Commun / Year: 2017
Title: Structure of SgK223 pseudokinase reveals novel mechanisms of homotypic and heterotypic association.
Authors: Patel, O. / Griffin, M.D.W. / Panjikar, S. / Dai, W. / Ma, X. / Chan, H. / Zheng, C. / Kropp, A. / Murphy, J.M. / Daly, R.J. / Lucet, I.S.
History
DepositionApr 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: 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 1.2Mar 6, 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: Tyrosine-protein kinase SgK223


Theoretical massNumber of molelcules
Total (without water)54,2301
Polymers54,2301
Non-polymers00
Water1629
1
A: Tyrosine-protein kinase SgK223

A: Tyrosine-protein kinase SgK223


Theoretical massNumber of molelcules
Total (without water)108,4602
Polymers108,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3350 Å2
ΔGint-32 kcal/mol
Surface area34360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.683, 144.683, 47.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tyrosine-protein kinase SgK223 / Sugen kinase 223


Mass: 54230.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SGK223 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86YV5, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: 0.1M Hepes pH 7.5, 1.6M NaH2PO4/KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
ReflectionResolution: 2.95→45.753 Å / Num. obs: 20160 / % possible obs: 98 % / Redundancy: 8.5 % / Biso Wilson estimate: 64.14 Å2 / Rmerge F all: 0.102 / CC1/2: 0.999 / Net I/av σ(I): 18.62 / Net I/σ(I): 3.85
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 8.38 % / Rmerge F all: 0.659 / Num. unique obs: 3203 / CC1/2: 0.893 / Net I/σ(I) all: 3.85

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.953→45.753 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 24.99
RfactorNum. reflection% reflection
Rfree0.2624 1749 8.68 %
Rwork0.2183 --
obs0.2221 20150 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.43 Å2 / Biso mean: 58.9107 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.953→45.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 0 9 2764
Biso mean---57.96 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032771
X-RAY DIFFRACTIONf_angle_d0.6523751
X-RAY DIFFRACTIONf_chiral_restr0.024426
X-RAY DIFFRACTIONf_plane_restr0.004482
X-RAY DIFFRACTIONf_dihedral_angle_d13.9981021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9528-3.03970.30691600.27481466162697
3.0397-3.13780.3221320.237215571689100
3.1378-3.24990.26081730.235114771650100
3.2499-3.380.28491610.230715691730100
3.38-3.53380.29961390.21215231662100
3.5338-3.720.26431180.196815761694100
3.72-3.9530.28361430.220515411684100
3.953-4.2580.24581530.195715281681100
4.258-4.68610.24041530.200715311684100
4.6861-5.36330.25571300.199715491679100
5.3633-6.75370.2431430.251315471690100
6.7537-45.75830.25581440.22515371681100

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