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- PDB-7pvw: Crystal structure of the intertwined dimer of the c-Src SH3 domai... -

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Entry
Database: PDB / ID: 7pvw
TitleCrystal structure of the intertwined dimer of the c-Src SH3 domain E93V-S94A-R95S-T96G-N112G-N113Y-T114N-E115H mutant
ComponentsIsoform 1 of Proto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homologynon-specific protein-tyrosine kinase / ACETATE ION / Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
Model detailsChimera construction c-Src-Abl 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: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
B: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4604
Polymers13,2062
Non-polymers2532
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Intertwined dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-27 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.037, 68.037, 46.183
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Isoform 1 of Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 6603.213 Da / Num. of mol.: 2 / Mutation: E93V, S94A, R95S,T96G, N112G, N113Y, T114N, E115H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00523-1, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.34 Å3/Da / Density % sol: 47.36 % / Mosaicity: 0.14 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.9 M ammonium sulfate, 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: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.5→19.64 Å / Num. obs: 19622 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Net I/σ(I): 17.9 / Num. measured all: 126662
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
1.5-1.536.61.00864819750.8380.4231.0942.1100
8.22-19.645.90.02971812210.0120.03148.292.2

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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: 4LE9

4le9


Resolution: 1.5→19.64 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 1939 5.09 %
Rwork0.1608 36119 -
obs0.1623 38058 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.14 Å2 / Biso mean: 32.9015 Å2 / Biso min: 18.25 Å2
Refinement stepCycle: final / Resolution: 1.5→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 38 85 1052
Biso mean--57.99 41.09 -
Num. residues----119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.25451620.23112540270299
1.54-1.580.27471380.21122616275499
1.58-1.630.20861110.18932583269499
1.63-1.680.2041180.19232598271699
1.68-1.740.24121380.19112567270599
1.74-1.810.23061770.1532514269199
1.81-1.890.1761500.13192594274499
1.89-1.990.22091400.186625692709100
1.99-2.110.17351340.161626232757100
2.11-2.280.20321200.169825802700100
2.28-2.510.19311140.174625992713100
2.51-2.870.19661680.184725712739100
2.87-3.610.19541310.1512581271299
3.61-19.640.15921380.139725842722100

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