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- PDB-3cqt: N53I V55L MUTANT of FYN SH3 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 3cqt
TitleN53I V55L MUTANT of FYN SH3 DOMAIN
ComponentsProto-oncogene tyrosine-protein kinase Fyn
KeywordsTRANSFERASE / beta barrel / ATP-binding / Developmental protein / Kinase / Lipoprotein / Manganese / Metal-binding / Myristate / Nucleotide-binding / Palmitate / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


forebrain development / extrinsic component of cytoplasmic side of plasma membrane / tubulin binding / cell surface receptor protein tyrosine kinase signaling pathway / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / regulation of cell shape / perikaryon ...forebrain development / extrinsic component of cytoplasmic side of plasma membrane / tubulin binding / cell surface receptor protein tyrosine kinase signaling pathway / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / regulation of cell shape / perikaryon / protein tyrosine kinase activity / cell differentiation / protein kinase activity / membrane raft / signaling receptor binding / innate immune response / ATP binding / metal ion binding / nucleus / cytosol
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 / 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 / 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
Tyrosine-protein kinase Fyn
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNeculai, A.M. / Zarrine-Afsar, A. / Howell, P.L. / Davidson, A. / Chan, H.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding.
Authors: Zarrine-Afsar, A. / Wallin, S. / Neculai, A.M. / Neudecker, P. / Howell, P.L. / Davidson, A.R. / Chan, H.S.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 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

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Fyn


Theoretical massNumber of molelcules
Total (without water)9,3371
Polymers9,3371
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.032, 52.032, 44.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Fyn / p59-Fyn


Mass: 9337.112 Da / Num. of mol.: 1 / Fragment: Fyn SH3 domain / Mutation: N53I, V55L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21*
References: UniProt: Q05876, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.88 Å3/Da / Density % sol: 34.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium Cacodylate, 1.4 M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 4, 2007 / Details: mirrors
RadiationMonochromator: Ni MIRROR 0.3 + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→45.06 Å / Num. all: 9568 / Num. obs: 8962 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.0728 / Rsym value: 0.0175 / Net I/σ(I): 53.07
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.1178 / Mean I/σ(I) obs: 33.05 / Rsym value: 0.031 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0036refinement
CrystalCleardata collection
XDSdata reduction
XDSdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1fyn

1fyn


Resolution: 1.6→45.06 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.464 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23652 435 4.9 %RANDOM
Rwork0.20743 ---
obs0.20881 8516 93.69 %-
all-9568 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms496 0 0 89 585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.934702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.042563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6624.44427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8831579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.935152
X-RAY DIFFRACTIONr_chiral_restr0.0740.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02411
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.2209
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2351
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5541.5312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9712493
X-RAY DIFFRACTIONr_scbond_it1.3053237
X-RAY DIFFRACTIONr_scangle_it1.8964.5209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 37 -
Rwork0.231 625 -
obs--96.78 %

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