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- PDB-8x2t: The Crystal Structure of FES from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x2t
TitleThe Crystal Structure of FES from Biortus.
ComponentsTyrosine-protein kinase Fes/Fps
KeywordsTRANSFERASE / Kinase / Tyrosine-protein kinase / ATP-binding / Lipid-binding / Nucleotide-binding
Function / homology
Function and homology information


positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle ...positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle / myoblast proliferation / cardiac muscle cell proliferation / regulation of cell differentiation / Sema3A PAK dependent Axon repulsion / regulation of cell adhesion / positive regulation of microtubule polymerization / immunoglobulin receptor binding / phosphatidylinositol binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / chemotaxis / microtubule cytoskeleton / regulation of cell population proliferation / regulation of cell shape / cytoplasmic vesicle / microtubule binding / protein tyrosine kinase activity / protein autophosphorylation / cell adhesion / focal adhesion / Golgi apparatus / ATP binding / cytoplasm / cytosol
Similarity search - Function
Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. ...Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 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
Similarity search - Domain/homology
Tyrosine-protein kinase Fes/Fps
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Pan, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of FES from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Pan, W.
History
DepositionNov 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fes/Fps


Theoretical massNumber of molelcules
Total (without water)46,4511
Polymers46,4511
Non-polymers00
Water84747
1
A: Tyrosine-protein kinase Fes/Fps

A: Tyrosine-protein kinase Fes/Fps


Theoretical massNumber of molelcules
Total (without water)92,9032
Polymers92,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15760 Å2
ΔGint-129 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.882, 29.952, 73.792
Angle α, β, γ (deg.)90.000, 107.674, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine-protein kinase Fes/Fps


Mass: 46451.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FES / Production host: Escherichia coli (E. coli) / References: UniProt: P07332
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M CaCl2, 0.1M Tris pH8.5, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979514 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979514 Å / Relative weight: 1
ReflectionResolution: 2.9→45.75 Å / Num. obs: 8125 / % possible obs: 87.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.014 / Net I/σ(I): 9.9
Reflection shellResolution: 2.9→2.98 Å / Rmerge(I) obs: 0.385 / Num. unique obs: 1352

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.748 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.783 / SU B: 24.072 / SU ML: 0.448 / Cross valid method: FREE R-VALUE / ESU R Free: 0.658
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3394 383 4.714 %
Rwork0.2695 7742 -
all0.273 --
obs-8125 87.159 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.99 Å2
Baniso -1Baniso -2Baniso -3
1--5.945 Å20 Å24.099 Å2
2--0.948 Å20 Å2
3---1.982 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 0 47 3059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0133061
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172955
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.6394125
X-RAY DIFFRACTIONr_angle_other_deg1.0241.5776800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3035370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52922.582182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29215581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3171525
X-RAY DIFFRACTIONr_chiral_restr0.0330.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
X-RAY DIFFRACTIONr_nbd_refined0.150.2589
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1550.22438
X-RAY DIFFRACTIONr_nbtor_refined0.130.21434
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.237
X-RAY DIFFRACTIONr_nbd_other0.1310.2206
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2880.24
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_mcbond_it0.4895.4671492
X-RAY DIFFRACTIONr_mcbond_other0.4895.4651491
X-RAY DIFFRACTIONr_mcangle_it0.918.1921858
X-RAY DIFFRACTIONr_mcangle_other0.918.1941859
X-RAY DIFFRACTIONr_scbond_it0.2795.5151569
X-RAY DIFFRACTIONr_scbond_other0.2795.5171570
X-RAY DIFFRACTIONr_scangle_it0.5638.2692267
X-RAY DIFFRACTIONr_scangle_other0.5638.2712268
X-RAY DIFFRACTIONr_lrange_it2.91962.6923269
X-RAY DIFFRACTIONr_lrange_other2.91862.7153270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.294270.294600X-RAY DIFFRACTION91.3994
2.975-3.0570.468320.319565X-RAY DIFFRACTION89.5052
3.057-3.1450.464220.328534X-RAY DIFFRACTION89.2456
3.145-3.2420.383220.317531X-RAY DIFFRACTION89.4822
3.242-3.3480.358250.28530X-RAY DIFFRACTION87.8165
3.348-3.4660.296280.276475X-RAY DIFFRACTION88.7125
3.466-3.5960.404190.265479X-RAY DIFFRACTION88.2979
3.596-3.7430.305310.246464X-RAY DIFFRACTION87.6106
3.743-3.9090.406200.247416X-RAY DIFFRACTION87.0259
3.909-4.0990.268180.252425X-RAY DIFFRACTION87.3767
4.099-4.3210.243200.218401X-RAY DIFFRACTION85.0505
4.321-4.5820.261200.22348X-RAY DIFFRACTION84.0183
4.582-4.8970.258170.236364X-RAY DIFFRACTION86.3946
4.897-5.2890.379160.232317X-RAY DIFFRACTION83.8791
5.289-5.7910.343190.305295X-RAY DIFFRACTION82.8496
5.791-6.4720.468150.32267X-RAY DIFFRACTION84.9398
6.472-7.4670.336130.288260X-RAY DIFFRACTION85.8491
7.467-9.130.32280.275201X-RAY DIFFRACTION84.2742
9.13-12.8470.30470.221170X-RAY DIFFRACTION83.8863
12.847-45.7480.70940.322100X-RAY DIFFRACTION78.1955

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