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- PDB-7pw2: Crystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E ... -

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Basic information

Entry
Database: PDB / ID: 7pw2
TitleCrystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E mutant
ComponentsNon-specific protein-tyrosine kinaseNon-receptor tyrosine kinase
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


GTPase activator activity / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of GTPase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / cytoplasm
Similarity search - Function
Bcr-Abl oncoprotein oligomerisation / Bcr-Abl oncoprotein oligomerisation domain superfamily / Bcr-Abl oncoprotein oligomerisation domain / Abr/Bcr / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / PH domain profile. / Pleckstrin homology domain. ...Bcr-Abl oncoprotein oligomerisation / Bcr-Abl oncoprotein oligomerisation domain superfamily / Bcr-Abl oncoprotein oligomerisation domain / Abr/Bcr / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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. / PH-like domain superfamily / 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
Non-specific protein-tyrosine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
Model detailsChimera construction Abl-c-Src SH3 domain
AuthorsCamara-Artigas, A. / Salinas Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2006-78020-R Spain
CitationJournal: To be published
Title: The effect of the hinge loops composition in the domain swapping of the SH3 domain
Authors: Camara-Artigas, A. / Salinas Garcia, M.C.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Non-specific protein-tyrosine kinase


Theoretical massNumber of molelcules
Total (without water)6,7211
Polymers6,7211
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.580, 42.580, 30.407
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Non-specific protein-tyrosine kinase / Non-receptor tyrosine kinase


Mass: 6721.397 Da / Num. of mol.: 1 / Mutation: V73E, A74S, S75R, G76T, D77E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCR/ABL fusion / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A9UF07, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.05 Å3/Da / Density % sol: 40.02 % / Mosaicity: 0.09 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0 M ammonium sulfate, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.1→17.44 Å / Num. obs: 21193 / % possible obs: 95.3 % / Redundancy: 2 % / Biso Wilson estimate: 17.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.022 / Rrim(I) all: 0.035 / Net I/σ(I): 9.9 / Num. measured all: 43012
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.1-1.1220.455213410830.6830.3850.61.697
6.03-17.442.10.0312401130.9920.0270.04118.980.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EG3

3eg3


Resolution: 1.1→17.44 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 34.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 1752 5.36 %
Rwork0.183 30963 -
obs0.1841 32715 75.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.6 Å2 / Biso mean: 27.5203 Å2 / Biso min: 14.31 Å2
Refinement stepCycle: final / Resolution: 1.1→17.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 0 51 472
Biso mean---36.89 -
Num. residues----57
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.130.32691520.27852412256476
1.13-1.160.26881350.24952401253675
1.16-1.20.26381190.21942372249176
1.2-1.240.2421500.22952404255476
1.24-1.290.22441230.21882418254177
1.29-1.350.26631290.19342390251976
1.35-1.420.23991410.19752371251275
1.42-1.510.19161410.21972478261978
1.51-1.630.23191680.21072286245474
1.63-1.790.1769880.19552460254876
1.79-2.050.17091230.19292396251975
2.05-2.580.19591550.17892300245574
2.58-17.440.19651280.16152275240372

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