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- PDB-7pvt: Crystal structure of the v-Src SH3 domain Q128R mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 7pvt
TitleCrystal structure of the v-Src SH3 domain Q128R mutant in complex with the synthetic peptide VSL12
Components
  • Tyrosine-protein kinase transforming protein Src
  • VSL12
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / ATP binding
Similarity search - Function
: / 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 / 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. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
DI(HYDROXYETHYL)ETHER / Tyrosine-protein kinase transforming protein Src
Similarity search - Component
Biological speciesRous sarcoma virus
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
Model detailsIntertwined dimer
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: Crystal structure of the v-Src SH3 domain Q128R mutant in complex with the synthetic peptide VSL12
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: Tyrosine-protein kinase transforming protein Src
B: VSL12
C: Tyrosine-protein kinase transforming protein Src
D: VSL12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5566
Polymers16,3584
Non-polymers1982
Water1,00956
1
A: Tyrosine-protein kinase transforming protein Src
B: VSL12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2853
Polymers8,1792
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5 kcal/mol
Surface area4130 Å2
2
C: Tyrosine-protein kinase transforming protein Src
D: VSL12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2713
Polymers8,1792
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-7 kcal/mol
Surface area4040 Å2
Unit cell
Length a, b, c (Å)51.227, 51.227, 46.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Tyrosine-protein kinase transforming protein Src / pp60v-src / p60-Src / v-Src


Mass: 6861.487 Da / Num. of mol.: 2 / Mutation: Q128R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin E)
Strain: Schmidt-Ruppin E / Gene: V-SRC / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P63185, non-specific protein-tyrosine kinase
#2: Protein/peptide VSL12


Mass: 1317.622 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.15 Å3/Da / Density % sol: 42.68 % / Mosaicity: 0 °
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4 M ammonium sulfate, 10% glicerol, 5% PEG300, 40 mM LiCl, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.6→17.18 Å / Num. obs: 17900 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 14.2 / Num. measured all: 116716 / Scaling rejects: 242
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
1.6-1.636.70.80259638950.790.3350.871.9100
8.76-17.186.10.068588970.9910.0320.0753389.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NER

7ner


Resolution: 1.6→17.18 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 1785 5.01 %
Rwork0.1781 33871 -
obs0.1794 35656 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.97 Å2 / Biso mean: 36.7025 Å2 / Biso min: 17.55 Å2
Refinement stepCycle: final / Resolution: 1.6→17.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 31 56 1112
Biso mean--69.59 37.91 -
Num. residues----131
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 (%)
1.6-1.640.351560.303426412797100
1.64-1.690.281880.288625692657100
1.69-1.750.26081360.246826192755100
1.75-1.810.22951760.224526102786100
1.81-1.880.22191320.209225852717100
1.88-1.960.23931320.157926722804100
1.97-2.070.17751320.144225872719100
2.07-2.20.2241280.176926392767100
2.2-2.370.1731920.196726472739100
2.37-2.610.18591760.20252522269897
2.61-2.980.24761400.19562571271198
2.98-3.750.20041560.165725862742100
3.75-17.180.17861410.151126232764100

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