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- PDB-6edf: Fragment of a tyrosine-protein kinase -

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Basic information

Entry
Database: PDB / ID: 6edf
TitleFragment of a tyrosine-protein kinase
ComponentsFYN
KeywordsTRANSFERASE / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / regulation of glutamate receptor signaling pathway / heart process / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / regulation of glutamate receptor signaling pathway / heart process / Activated NTRK2 signals through FYN / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / reelin-mediated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of protein localization to membrane / cellular response to L-glutamate / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / FLT3 signaling through SRC family kinases / activated T cell proliferation / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / negative regulation of dendritic spine maintenance / feeding behavior / Co-stimulation by CD28 / Nephrin family interactions / natural killer cell activation / DCC mediated attractive signaling / EPH-Ephrin signaling / Ephrin signaling / dendritic spine maintenance / CD28 dependent Vav1 pathway / dendrite morphogenesis / tau-protein kinase activity / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / PECAM1 interactions / response to amyloid-beta / cellular response to glycine / FCGR activation / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / glial cell projection / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / CD28 dependent PI3K/Akt signaling / alpha-tubulin binding / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / forebrain development / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / T cell costimulation / Signaling by ERBB2 / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / learning / Cell surface interactions at the vascular wall / actin filament / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / G protein-coupled receptor binding / modulation of chemical synaptic transmission / protein catabolic process / Signaling by SCF-KIT / peptidyl-tyrosine phosphorylation / negative regulation of protein catabolic process / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / tau protein binding / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / cellular response to amyloid-beta / neuron migration / Signaling by CSF1 (M-CSF) in myeloid cells / calcium ion transport / Constitutive Signaling by Aberrant PI3K in Cancer / disordered domain specific binding
Similarity search - Function
: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily ...: / Fyn/Yrk, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTempel, W. / Huang, H. / Sochirca, I. / Liu, K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Sidhu, S.S. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Fragment of a tyrosine-protein kinase
Authors: Tempel, W. / Huang, H. / Sochirca, I. / Liu, K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Sidhu, S.S. / Min, J.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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: FYN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,93616
Polymers8,5911
Non-polymers34415
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint1 kcal/mol
Surface area5850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.991, 36.233, 38.646
Angle α, β, γ (deg.)90.000, 99.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FYN / Tyrosine-protein kinase Fyn


Mass: 8591.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: custom pHH0239 / Production host: Escherichia coli (E. coli) / Strain (production host): SS320 (Genentech)
References: UniProt: P06241*PLUS, non-specific protein-tyrosine 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: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 12, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→36.23 Å / Num. obs: 12781 / % possible obs: 98.4 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.063 / Net I/σ(I): 16.5 / Num. measured all: 47091 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.423.10.417435640.8170.2720.4873.387.7
7.54-36.233.30.026303920.9980.0170.03141.998.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDS0.7.2data reduction
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UF4

3uf4


Resolution: 1.4→26.27 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.003 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.059
Details: ARP/WARP was used for map improvement. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Residue numbering follows the precedence from PDB entry 3CQT.
RfactorNum. reflection% reflection
Rfree0.1721 619 4.8 %
Rwork0.1434 --
obs0.1448 12154 98.24 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 47.96 Å2 / Biso mean: 12.097 Å2 / Biso min: 5.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å2-0.38 Å2
2---0.26 Å20 Å2
3---0.93 Å2
Refinement stepCycle: final / Resolution: 1.4→26.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms587 0 20 61 668
Biso mean--22.96 20.05 -
Num. residues----77
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.014635
X-RAY DIFFRACTIONr_bond_other_d0.0010.017557
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.662869
X-RAY DIFFRACTIONr_angle_other_deg1.1021.6571302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.004584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.29120.62532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4241596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.296155
X-RAY DIFFRACTIONr_chiral_restr0.10.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02127
X-RAY DIFFRACTIONr_mcbond_it1.9141.193321
X-RAY DIFFRACTIONr_mcbond_other1.8091.183320
X-RAY DIFFRACTIONr_mcangle_it2.791.77402
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.165 42 -
Rwork0.226 783 -
all-825 -
obs--87.86 %

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