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- PDB-4f5a: Triple mutant Src SH2 domain bound to phosphate ion -

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Basic information

Entry
Database: PDB / ID: 4f5a
TitleTriple mutant Src SH2 domain bound to phosphate ion
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / SH2 domain / Cell signalling / phosphotyrosine
Function / homology
Function and homology information


positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of ovarian follicle development / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of ovarian follicle development / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / response to mineralocorticoid / positive regulation of dephosphorylation / ERBB2 signaling pathway / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / positive regulation of protein transport / Regulation of gap junction activity / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / regulation of vascular permeability / positive regulation of protein processing / positive regulation of integrin activation / Activated NTRK2 signals through FYN / negative regulation of focal adhesion assembly / skeletal muscle cell proliferation / : / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / osteoclast development / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / response to acidic pH / connexin binding / focal adhesion assembly / signal complex assembly / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / adherens junction organization / DCC mediated attractive signaling / EPH-Ephrin signaling / odontogenesis / myoblast proliferation / Ephrin signaling / cellular response to peptide hormone stimulus / negative regulation of mitochondrial depolarization / podosome / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / Regulation of KIT signaling / postsynaptic specialization, intracellular component / Signaling by ALK / leukocyte migration / GP1b-IX-V activation signalling / CTLA4 inhibitory signaling / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase activator activity / oogenesis / Receptor Mediated Mitophagy / DNA biosynthetic process / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / Signaling by EGFR / positive regulation of epithelial cell migration / stress fiber assembly / positive regulation of smooth muscle cell migration / stimulatory C-type lectin receptor signaling pathway / regulation of cell-cell adhesion / cellular response to platelet-derived growth factor stimulus / dendritic growth cone / regulation of heart rate by cardiac conduction / RUNX2 regulates osteoblast differentiation / Recycling pathway of L1 / uterus development / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / neurotrophin TRK receptor signaling pathway / phospholipase binding / negative regulation of telomere maintenance via telomerase / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / Long-term potentiation / negative regulation of anoikis / RET signaling / FCGR activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / positive regulation of bone resorption
Similarity search - Function
SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...SH2 domain / SHC Adaptor Protein / : / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKaneko, T. / Huang, H. / Cao, X. / Li, C. / Voss, C. / Sidhu, S.S. / Li, S.S.
CitationJournal: Sci.Signal. / Year: 2012
Title: Superbinder SH2 Domains Act as Antagonists of Cell Signaling.
Authors: Kaneko, T. / Huang, H. / Cao, X. / Li, X. / Li, C. / Voss, C. / Sidhu, S.S. / Li, S.S.
History
DepositionMay 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7942
Polymers12,6991
Non-polymers951
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.980, 66.980, 46.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Detailsbiological unit is the same as asym.

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Components

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


Mass: 12699.316 Da / Num. of mol.: 1 / Fragment: SH2 domain / Mutation: T183V/C188A/K206L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12931
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1 M Tris-HCl, 18% PEG6000, 0.2 M lithium chloride, pH 7.6, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 114 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2011
RadiationMonochromator: Graded multilayer (osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→58.006 Å / Num. all: 11161 / Num. obs: 11161 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.038 / Net I/σ(I): 27.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.95.80.2672.9947316410.267100
1.9-2.015.80.1515.1891915310.151100
2.01-2.155.90.0918857614590.091100
2.15-2.325.90.06610.7791413350.066100
2.32-2.5560.04914741812390.049100
2.55-2.8560.03716.5672311160.037100
2.85-3.296.10.03118.2610910060.031100
3.29-4.0360.0311850568390.03199.9
4.03-5.695.70.03218.437436570.03298.7
5.69-27.2275.10.03416.917143380.03489.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.07 Å27.23 Å
Translation2.07 Å27.23 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→58.006 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2685 / WRfactor Rwork: 0.2181 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8157 / SU B: 7.506 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1387 / SU Rfree: 0.1333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 530 4.8 %RANDOM
Rwork0.2052 ---
all0.2072 11144 --
obs0.2072 11144 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.18 Å2 / Biso mean: 34.1007 Å2 / Biso min: 11.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.4 Å20 Å2
2--0.81 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→58.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 5 63 935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021888
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9531199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.40122.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14815153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.415158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02671
X-RAY DIFFRACTIONr_mcbond_it0.8091.5534
X-RAY DIFFRACTIONr_mcangle_it1.4232857
X-RAY DIFFRACTIONr_scbond_it2.4783354
X-RAY DIFFRACTIONr_scangle_it4.0054.5342
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 45 -
Rwork0.281 790 -
all-835 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -15.962 Å / Origin y: 19.449 Å / Origin z: 0.677 Å
111213212223313233
T0.0622 Å20.0258 Å20.0165 Å2-0.0887 Å20.0213 Å2--0.0274 Å2
L2.4369 °2-0.2446 °20.4802 °2-5.397 °2-0.394 °2--4.7928 °2
S-0.0918 Å °-0.144 Å °-0.0803 Å °0.0639 Å °0.1727 Å °0.0579 Å °-0.2539 Å °-0.357 Å °-0.0809 Å °

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