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- PDB-7nes: Crystal structure of the v-Src SH3 domain N117D-V124L mutant -

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Basic information

Entry
Database: PDB / ID: 7nes
TitleCrystal structure of the v-Src SH3 domain N117D-V124L mutant
Componentsv-Src SH3 domain
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homologyGLYCINE
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
Model detailsIntertwined dimer
AuthorsCamara-Artigas, A. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain.
Authors: Salinas-Garcia, M.C. / Plaza-Garrido, M. / Camara-Artigas, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2021
Title: The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain
Authors: Salinas-Garcia, M.C. / Plaza-Garrido, M. / Camara-Artigas, A.
History
DepositionFeb 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: v-Src SH3 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9232
Polymers6,8471
Non-polymers751
Water1,20767
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 area3950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.171, 37.171, 65.824
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-363-

HOH

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Components

#1: Protein v-Src SH3 domain


Mass: 6847.434 Da / Num. of mol.: 1 / Mutation: N117D, V124L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.92 Å3/Da / Density % sol: 35.84 % / Mosaicity: 0.12 °
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8M ammonium sulfate, 0.5M glycine and 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.35→18.59 Å / Num. obs: 12108 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Net I/σ(I): 18.1
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
1.35-1.377.90.76147176000.9220.290.8152.5100
7.39-18.595.70.028519910.9990.0120.0355.295.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
PHENIXdev-3951refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 6 / Resolution: 1.35→18.59 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1827 1144 5.13 %
Rwork0.1579 21176 -
obs0.1593 12056 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.89 Å2 / Biso mean: 21.8414 Å2 / Biso min: 12.98 Å2
Refinement stepCycle: final / Resolution: 1.35→18.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms467 0 7 67 541
Biso mean--61.03 30.68 -
Num. residues----58
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.410.24621540.22932628278299
1.41-1.490.19161170.19732694281199
1.49-1.580.18771100.180626562766100
1.58-1.70.1861240.155926632787100
1.7-1.870.20851140.195526792793100
1.87-2.140.16071740.154226032777100
2.14-2.70.17481860.156226262812100
2.7-18.590.18481650.141126272792100

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