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- PDB-6ipz: Fyn SH3 domain R96W mutant, crystallized with 18-crown-6 -

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Basic information

Entry
Database: PDB / ID: 6ipz
TitleFyn SH3 domain R96W mutant, crystallized with 18-crown-6
ComponentsTyrosine-protein kinase Fyn
KeywordsPROTEIN BINDING / kinase / SH3 domain / 18-crown-6 / crown ether
Function / homology
Function and homology information


response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / Platelet Adhesion to exposed collagen / G protein-coupled glutamate receptor signaling pathway / CD28 co-stimulation / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / feeding behavior / Nef and signal transduction / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / Nephrin family interactions / DCC mediated attractive signaling / dendrite morphogenesis / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / leukocyte migration / phospholipase activator activity / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / glial cell projection / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / Sema3A PAK dependent Axon repulsion / cellular response to glycine / alpha-tubulin binding / FCGR activation / EPH-ephrin mediated repulsion of cells / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / 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 / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / Signaling by ERBB2 / negative regulation of protein ubiquitination / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / EPHB-mediated forward signaling / T cell costimulation / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / ephrin receptor binding / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / axon guidance / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / protein catabolic process / modulation of chemical synaptic transmission / tau protein binding / Signaling by SCF-KIT / negative regulation of protein catabolic process / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / calcium ion transport / Signaling by CSF1 (M-CSF) in myeloid cells / 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 / SH3 type barrels. / Src homology 3 domains ...: / Fyn/Yrk, SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / 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 / 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
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.576 Å
AuthorsArold, S.T. / Aljedani, S.S. / Shahul Hameed, U.F.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other governmentKAUST - BAS/1/1056-01 Saudi Arabia
CitationJournal: Biochem.J. / Year: 2021
Title: Synergy and allostery in ligand binding by HIV-1 Nef.
Authors: Aldehaiman, A. / Momin, A.A. / Restouin, A. / Wang, L. / Shi, X. / Aljedani, S. / Opi, S. / Lugari, A. / Shahul Hameed, U.F. / Ponchon, L. / Morelli, X. / Huang, M. / Dumas, C. / Collette, Y. / Arold, S.T.
History
DepositionNov 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: Tyrosine-protein kinase Fyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3783
Polymers7,8501
Non-polymers5292
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.490, 51.490, 51.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11Z-312-

HOH

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Components

#1: Protein Tyrosine-protein kinase Fyn


Mass: 7849.575 Da / Num. of mol.: 1 / Fragment: UNP residues 82-144 / Mutation: R96W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6


Mass: 264.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.08M Sodium acetate trihydrate pH 4.6, 1.6M Ammonium sulfate, 20%(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.576→36.536 Å / Num. obs: 10112 / % possible obs: 99.83 % / Redundancy: 25.6 % / Biso Wilson estimate: 34.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06273 / Rpim(I) all: 0.01267 / Rrim(I) all: 0.06403 / Net I/σ(I): 29.66
Reflection shellResolution: 1.576→1.633 Å / Redundancy: 24.9 % / Rmerge(I) obs: 2.542 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 988 / CC1/2: 0.565 / Rpim(I) all: 0.5147 / Rrim(I) all: 2.595 / % possible all: 98.38

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H0F

3h0f


Resolution: 1.576→36.536 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.45
RfactorNum. reflection% reflection
Rfree0.2088 506 5.01 %
Rwork0.1902 --
obs0.1912 10095 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.96 Å2 / Biso mean: 49.1487 Å2 / Biso min: 27.37 Å2
Refinement stepCycle: final / Resolution: 1.576→36.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms503 0 84 23 610
Biso mean--78.08 46.87 -
Num. residues----63
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5763-1.73490.30151240.28192333245799
1.7349-1.9860.2541240.227523572481100
1.986-2.5020.2211250.201823782503100
2.502-36.54530.1961330.177625212654100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3993-2.24690.83612.6728-1.43410.8211-0.1693-0.2432-0.5-0.03440.2560.4822-0.66690.03530.03680.8892-0.1892-0.00810.4993-0.08940.468210.57730.9760.757
20.4122-0.0781-0.29430.4408-0.41170.7339-0.01940.3437-0.0783-0.5328-0.044-0.37920.16380.04430.00010.38920.00250.02340.32580.00340.350920.31647.79-1.398
31.30381.2707-0.56691.393-0.56951.95990.0176-0.10020.0144-0.07490.06760.19960.1461-0.19300.3062-0.0192-0.00290.33010.00610.335314.34548.9463.738
40.0826-0.13130.12750.2037-0.21170.33680.379-0.47570.5691-0.2189-0.46451.0569-0.4302-0.6594-0.00220.91090.1533-0.11830.75560.02180.594.82549.287-5.194
50.1902-0.1423-0.13030.2602-0.04690.2023-0.08260.1271-0.14990.120.06230.4744-0.0126-0.18620.00010.3633-0.0266-0.00070.37950.02710.378310.02246.1611.679
61.0610.4429-0.38471.1123-0.65230.698-0.0090.0531-0.2249-0.2070.08580.14770.3688-0.2956-0.00490.3954-0.0222-0.00520.33280.00820.322715.36944.1170.138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN Z AND RESID 81:86 )Z81 - 86
2X-RAY DIFFRACTION2( CHAIN Z AND RESID 87:94 )Z87 - 94
3X-RAY DIFFRACTION3( CHAIN Z AND RESID 95:113 )Z95 - 113
4X-RAY DIFFRACTION4( CHAIN Z AND RESID 114:118 )Z114 - 118
5X-RAY DIFFRACTION5( CHAIN Z AND RESID 119:124 )Z119 - 124
6X-RAY DIFFRACTION6( CHAIN Z AND RESID 125:143 )Z125 - 143

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