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- PDB-7ner: Crystal structure of the v-Src SH3 domain Q128R mutant -

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Basic information

Entry
Database: PDB / ID: 7ner
TitleCrystal structure of the v-Src SH3 domain Q128R mutant
Componentsv-Src SH3 domain
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)7,1523
Polymers6,8611
Non-polymers2902
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-10 kcal/mol
Surface area4090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.342, 34.978, 31.140
Angle α, β, γ (deg.)90.000, 96.402, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein v-Src SH3 domain


Mass: 6861.487 Da / Num. of mol.: 1 / Mutation: Q128R
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.79 Å3/Da / Density % sol: 31.37 % / Mosaicity: 0.09 °
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.1 M ammonium sulfate, 5% PEG 200, 10% glycerol, 40 mM LiCl and 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.55→30.95 Å / Num. obs: 6888 / % possible obs: 98 % / Redundancy: 2.7 % / Biso Wilson estimate: 14.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.039 / Rrim(I) all: 0.067 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.630.338262410100.860.2470.4212.496.8
4.9-30.950.0265802270.9990.0190.03229.293.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimless0.6.3data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XVN

6xvn


Resolution: 1.55→19.08 Å / SU ML: 0.0741 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 18.649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1622 598 4.86 %
Rwork0.1474 11717 -
obs0.1481 6879 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.69 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms478 0 18 48 544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0102508
X-RAY DIFFRACTIONf_angle_d0.8925690
X-RAY DIFFRACTIONf_chiral_restr0.052273
X-RAY DIFFRACTIONf_plane_restr0.006684
X-RAY DIFFRACTIONf_dihedral_angle_d14.0303175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.710.18481640.18892836X-RAY DIFFRACTION88.57
1.71-1.950.18641480.16212944X-RAY DIFFRACTION90.62
1.95-2.460.17551320.14942956X-RAY DIFFRACTION90.8
2.46-19.080.14551540.13482981X-RAY DIFFRACTION92.18

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