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- PDB-7net: Crystal structure of the v-Src SH3 domain W95R-I96T mutant -

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Basic information

Entry
Database: PDB / ID: 7net
TitleCrystal structure of the v-Src SH3 domain W95R-I96T mutant
Componentsv-Src SH3 domain
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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

Downloads & links

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Assembly

Deposited unit
A: v-Src SH3 domain
B: v-Src SH3 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2538
Polymers13,5832
Non-polymers6716
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-38 kcal/mol
Surface area6510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.648, 46.648, 127.967
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 84 through 93 or resid 96...
21(chain C and (resid 84 through 93 or resid 96...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 84 through 93 or resid 96...A84 - 93
121(chain A and (resid 84 through 93 or resid 96...A96 - 98
131(chain A and (resid 84 through 93 or resid 96...A100 - 112
141(chain A and (resid 84 through 93 or resid 96...A114 - 140
211(chain C and (resid 84 through 93 or resid 96...C84 - 93
221(chain C and (resid 84 through 93 or resid 96...C96 - 98
231(chain C and (resid 84 through 93 or resid 96...C100 - 109
241(chain C and (resid 84 through 93 or resid 96...C1
251(chain C and (resid 84 through 93 or resid 96...C1
261(chain C and (resid 84 through 93 or resid 96...C1
271(chain C and (resid 84 through 93 or resid 96...C1
281(chain C and (resid 84 through 93 or resid 96...C1

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Components

#1: Protein v-Src SH3 domain


Mass: 6791.352 Da / Num. of mol.: 2 / Mutation: W95R, I96T
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: 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: 2.96 Å3/Da / Density % sol: 58.43 % / Mosaicity: 0.08 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M ammonium sulfate, 5% PEG 300, 10% glycerol, 40 mM LiCl and 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→19.95 Å / Num. obs: 24714 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.016 / Rrim(I) all: 0.031 / Net I/σ(I): 20.3
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
1.5-1.532.30.425230610070.8170.3260.541.983.3
8.22-19.953.50.0295451550.9980.0180.03450.892.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.19.1-4122refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XVO

6xvo


Resolution: 1.5→19.95 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0.29 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 2333 4.99 %
Rwork0.1846 44450 -
obs0.1851 24656 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.95 Å2 / Biso mean: 42.7025 Å2 / Biso min: 18.62 Å2
Refinement stepCycle: final / Resolution: 1.5→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 97 67 1067
Biso mean--57.92 43.46 -
Num. residues----114
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A462X-RAY DIFFRACTION8.595TORSIONAL
12B462X-RAY DIFFRACTION8.595TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.530.29511040.24741987209172
1.53-1.560.2763950.22962278237381
1.56-1.60.23961140.22012581269592
1.6-1.640.27561600.20642639279996
1.64-1.680.21651320.20662732286497
1.68-1.730.20611290.17932681281096
1.73-1.790.19721270.17472686281395
1.79-1.850.221430.20062657280096
1.85-1.930.1491100.16582739284997
1.93-2.020.20261560.14972690284697
2.02-2.120.1341940.18972740283496
2.12-2.250.17671370.19372613275095
2.25-2.430.21681760.19132707288398
2.43-2.670.21161980.20722636283497
2.67-3.060.21851460.21112694284097
3.06-3.850.21231370.16542725286297
3.85-19.950.16311750.1762665284097

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