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- PDB-4dgx: LEOPARD Syndrome-Associated SHP2/Y279C mutant -

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Basic information

Entry
Database: PDB / ID: 4dgx
TitleLEOPARD Syndrome-Associated SHP2/Y279C mutant
ComponentsTyrosine-protein phosphatase non-receptor type 11
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / cerebellar cortex formation ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / cerebellar cortex formation / negative regulation of neutrophil activation / positive regulation of hormone secretion / regulation of protein export from nucleus / positive regulation of ossification / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / hormone metabolic process / Signaling by Leptin / MET activates PTPN11 / negative regulation of chondrocyte differentiation / Regulation of RUNX1 Expression and Activity / Regulation of T cell activation by CD28 family / face morphogenesis / Signal regulatory protein family interactions / ERBB signaling pathway / platelet formation / megakaryocyte development / organ growth / triglyceride metabolic process / peptide hormone receptor binding / negative regulation of type I interferon production / Interleukin-20 family signaling / Co-inhibition by CTLA4 / PI-3K cascade:FGFR3 / Interleukin-6 signaling / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / Prolactin receptor signaling / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / PECAM1 interactions / neurotrophin TRK receptor signaling pathway / inner ear development / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PI3K Cascade / ephrin receptor signaling pathway / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / regulation of protein-containing complex assembly / negative regulation of insulin secretion / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / cell adhesion molecule binding / GPVI-mediated activation cascade / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / hormone-mediated signaling pathway / T cell costimulation / FLT3 Signaling / phosphotyrosine residue binding / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cellular response to epidermal growth factor stimulus / positive regulation of mitotic cell cycle / Downstream signal transduction / axonogenesis / positive regulation of interferon-beta production / protein tyrosine kinase binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / DNA damage checkpoint signaling / integrin-mediated signaling pathway / positive regulation of D-glucose import / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / insulin receptor binding / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYu, Z.H. / Xu, J. / Walls, C.D. / Chen, L. / Zhang, S. / Wu, L. / Wang, L.N. / Liu, S.J. / Zhang, Z.Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Mechanistic Insights into LEOPARD Syndrome-Associated SHP2 Mutations.
Authors: Yu, Z.H. / Xu, J. / Walls, C.D. / Chen, L. / Zhang, S. / Zhang, R. / Wu, L. / Wang, L. / Liu, S. / Zhang, Z.Y.
History
DepositionJan 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2May 1, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 11


Theoretical massNumber of molelcules
Total (without water)61,7021
Polymers61,7021
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.140, 225.120, 40.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

21A-745-

HOH

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 11 / SRC homology 2 (SH2)-domain containing protein tyrosine phosphatase-2 / SHP2 / Protein-tyrosine ...SRC homology 2 (SH2)-domain containing protein tyrosine phosphatase-2 / SHP2 / Protein-tyrosine phosphatase 1D / PTP-1D / Protein-tyrosine phosphatase 2C / PTP-2C / SH-PTP2 / SHP-2 / SH-PTP3


Mass: 61701.609 Da / Num. of mol.: 1
Fragment: N-SH2, C-SH2, and PTP domains (UNP residues 1-532)
Mutation: Y279C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pET21A+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 20% PEG3350, 300 mM potassium formate, 10 mM calcium chloride, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 23621 / Num. obs: 23562 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 31.07
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.658 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→34.875 Å / SU ML: 0.34 / σ(F): 1.44 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 1177 5 %RANDOM
Rwork0.2088 ---
obs0.2117 23522 99.78 %-
all-23564 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.843 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.3678 Å20 Å20 Å2
2--9.2971 Å2-0 Å2
3---3.0707 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 0 183 4217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084123
X-RAY DIFFRACTIONf_angle_d1.1155561
X-RAY DIFFRACTIONf_chiral_restr0.074598
X-RAY DIFFRACTIONf_plane_restr0.004724
X-RAY DIFFRACTIONf_dihedral_angle_d16.1831557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3-2.40470.35551460.305727532899100
2.4047-2.53140.3071430.281327212864100
2.5314-2.68990.38541440.272927252869100
2.6899-2.89750.3651460.264127862932100
2.8975-3.1890.31571460.2327622908100
3.189-3.650.23791480.194728042952100
3.65-4.59690.21051490.162628472996100
4.5969-34.87870.23571550.18952947310299

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