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- PDB-7pvv: Crystal structure of the Abl SH3 domain G92N-Y93N-N94T-H95E mutant -

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Basic information

Entry
Database: PDB / ID: 7pvv
TitleCrystal structure of the Abl SH3 domain G92N-Y93N-N94T-H95E mutant
ComponentsBcr-abl1 e6a2 chimeric protein
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


GTPase activator activity / guanyl-nucleotide exchange factor activity / signal transduction / membrane / cytosol
Similarity search - Function
Abr/Bcr / Tyrosine-protein kinase ABL, SH2 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. ...Abr/Bcr / Tyrosine-protein kinase ABL, SH2 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Bcr-abl1 e6a2 chimeric protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 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: Bcr-abl1 e6a2 chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7323
Polymers6,4761
Non-polymers2562
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.886, 47.403, 75.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-202-

PGE

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Components

#1: Protein Bcr-abl1 e6a2 chimeric protein


Mass: 6476.116 Da / Num. of mol.: 1 / Mutation: G92N, Y93N, N94T, H95E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCR-ABL1 / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2RQD6
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.45 % / Mosaicity: 0.07 °
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.6 M ammonium sulfate, 5% PEG200, 10% Glicerol, 40 mM LiCl, 0.1M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.82→19.9 Å / Num. obs: 7019 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 28.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.019 / Rrim(I) all: 0.042 / Net I/σ(I): 14.8 / Num. measured all: 33491
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
1.82-1.864.10.43717284170.8880.2430.5022.299.7
8.92-19.93.80.02265690.9990.0110.02232.690.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EG3

3eg3


Resolution: 1.82→19.9 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.51 / Phase error: 32.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 610 4.72 %
Rwork0.2096 12317 -
obs0.2105 7015 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.44 Å2 / Biso mean: 39.7719 Å2 / Biso min: 20.03 Å2
Refinement stepCycle: final / Resolution: 1.82→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms432 0 41 40 513
Biso mean--43.37 41.49 -
Num. residues----57
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.82-2.290.27461460.236231403286
2.29-19.90.22311860.212232103396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTIONA99 - 106A
2X-RAY DIFFRACTIONA107 - 120A
3X-RAY DIFFRACTIONA63 - 83A
4X-RAY DIFFRACTIONA84 - 89A
5X-RAY DIFFRACTIONA90 - 98A

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