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- PDB-3eac: Crystal structure of SH2 domain of Human Csk (carboxyl-terminal s... -

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Basic information

Entry
Database: PDB / ID: 3eac
TitleCrystal structure of SH2 domain of Human Csk (carboxyl-terminal src kinase), Oxidized form.
ComponentsTyrosine-protein kinase CSK
KeywordsTRANSFERASE / SH2 / CSK / DISULFIDE / OXIDIZED / Reduced / ATP-binding / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of low-density lipoprotein particle clearance / proline-rich region binding / negative regulation of bone resorption / adherens junction organization / negative regulation of phagocytosis / cellular response to peptide hormone stimulus / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation ...negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of low-density lipoprotein particle clearance / proline-rich region binding / negative regulation of bone resorption / adherens junction organization / negative regulation of phagocytosis / cellular response to peptide hormone stimulus / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / RHOH GTPase cycle / PD-1 signaling / GAB1 signalosome / Negative regulation of FLT3 / T cell costimulation / Integrin signaling / protein tyrosine kinase binding / non-specific protein-tyrosine kinase / Signaling by high-kinase activity BRAF mutants / non-membrane spanning protein tyrosine kinase activity / MAP2K and MAPK activation / negative regulation of ERK1 and ERK2 cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / T cell receptor signaling pathway / protein phosphatase binding / protein tyrosine kinase activity / adaptive immune response / negative regulation of cell population proliferation / protein phosphorylation / extracellular exosome / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CSK-like, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...CSK-like, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
Tyrosine-protein kinase CSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsLiu, D. / Seidel, R.D. / Cowburn, D.
CitationJournal: Biophys Rep / Year: 2016
Title: Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase.
Authors: Liu, D. / Cowburn, D.
History
DepositionAug 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 10, 2014Group: Version format compliance
Revision 1.3Jul 20, 2016Group: Database references
Revision 1.4Dec 14, 2016Group: Database references
Revision 1.5Aug 30, 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: Tyrosine-protein kinase CSK


Theoretical massNumber of molelcules
Total (without water)12,1631
Polymers12,1631
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.114, 48.025, 49.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase CSK / C-SRC kinase / Protein-tyrosine kinase CYL


Mass: 12162.913 Da / Num. of mol.: 1 / Fragment: SH2 Domain (UNP residues 73 to 178)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3) / Gene: CSK / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P41240, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.83 Å3/Da / Density % sol: 32.67 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.3
Details: 22% PEG 4000, 100 mM Bis-Tris, pH 7.3., EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 26, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 22360 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Biso Wilson estimate: 10.284 Å2
Reflection shellHighest resolution: 1.37 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K9A, sh2 part

1k9a


Resolution: 1.37→29.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.053 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21686 987 5.1 %RANDOM
Rwork0.20893 ---
all0.20934 18349 --
obs0.20934 18298 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.37→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 0 106 925
LS refinement shellResolution: 1.37→1.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 72 -
Rwork0.297 1333 -
obs--99.93 %

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