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- PDB-7a3c: Crystal structure of the c-Src SH3 domain mutant L100I at pH 3.0 -

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Basic information

Entry
Database: PDB / ID: 7a3c
TitleCrystal structure of the c-Src SH3 domain mutant L100I at pH 3.0
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homology
Function and homology information


connexin binding / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / immune system process / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell junction / epidermal growth factor receptor signaling pathway / cell-cell junction ...connexin binding / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / immune system process / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell junction / epidermal growth factor receptor signaling pathway / cell-cell junction / protein tyrosine kinase activity / protein phosphatase binding / cytoskeleton / regulation of cell cycle / cell differentiation / cell adhesion / endosome membrane / mitochondrial inner membrane / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol
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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCamara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: To be published
Title: Crystal structure of the c-Src SH3 domain mutant L100I at pH 3.0
Authors: Camara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C.
History
DepositionAug 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: 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: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
C: Proto-oncogene tyrosine-protein kinase Src
D: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,78610
Polymers27,2254
Non-polymers5616
Water2,252125
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9913
Polymers6,8061
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9953
Polymers6,8061
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8982
Polymers6,8061
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9022
Polymers6,8061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.477, 92.399, 37.594
Angle α, β, γ (deg.)90.000, 102.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6806.364 Da / Num. of mol.: 4 / Mutation: S94A, T98D, V111L, N113S, T114S
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, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 47.37 % / Mosaicity: 0.27 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3
Details: 5 mM beta-cyclodextrin, 1.5 M ammomium sulfate, 0.1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→19.56 Å / Num. obs: 33367 / % possible obs: 88.9 % / Redundancy: 2.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.032 / Rrim(I) all: 0.054 / Net I/σ(I): 7.1
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
1.8-1.8420.4715497760.7780.3540.591157.8
9-19.562.30.023611550.9980.0150.02518.481.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZ4

4jz4


Resolution: 1.8→19.56 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.16 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1721 5.16 %
Rwork0.1904 31646 -
obs0.1922 33367 73.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.45 Å2 / Biso mean: 33.387 Å2 / Biso min: 17.5 Å2
Refinement stepCycle: final / Resolution: 1.8→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 66 125 2043
Biso mean--50.28 37.2 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.3305510.28811618166944
1.85-1.910.25841250.26731910203554
1.91-1.980.26041440.25412644278872
1.98-2.060.25881510.22272845299679
2.06-2.150.22481590.20692735289478
2.15-2.270.2651620.19432777293977
2.27-2.410.24251270.19222843297079
2.41-2.60.21011680.20512880304879
2.6-2.860.2271770.19542802297978
2.86-3.270.20191680.19352853302180
3.27-4.110.18971590.16352831299078
4.11-19.560.25991300.17422908303880

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