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- PDB-1fpr: CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOM... -

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Basic information

Entry
Database: PDB / ID: 1fpr
TitleCRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOMAIN OF SHP-1 AND AN IN VITRO PEPTIDE SUBSTRATE PY469 DERIVED FROM SHPS-1.
Components
  • PEPTIDE PY469
  • PROTEIN-TYROSINE PHOSPHATASE 1C
KeywordsSIGNALING PROTEIN / protein tyrosine phosphatase / substrate specificity / residue shift
Function / homology
Function and homology information


negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / negative regulation of inflammatory response to wounding / phosphorylation-dependent protein binding / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex ...negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / regulation of B cell differentiation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / negative regulation of inflammatory response to wounding / phosphorylation-dependent protein binding / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Costimulation by the CD28 family / Signal regulatory protein family interactions / platelet formation / negative regulation of T cell receptor signaling pathway / megakaryocyte development / negative regulation of MAPK cascade / Regulation of KIT signaling / Signaling by ALK / Platelet sensitization by LDL / regulation of G1/S transition of mitotic cell cycle / PECAM1 interactions / regulation of type I interferon-mediated signaling pathway / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PD-1 signaling / Interleukin receptor SHC signaling / Nuclear events stimulated by ALK signaling in cancer / hematopoietic progenitor cell differentiation / Regulation of IFNG signaling / T cell proliferation / negative regulation of T cell proliferation / Growth hormone receptor signaling / cell adhesion molecule binding / GPVI-mediated activation cascade / T cell costimulation / phosphotyrosine residue binding / SH2 domain binding / protein dephosphorylation / protein-tyrosine-phosphatase / regulation of ERK1 and ERK2 cascade / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / cytokine-mediated signaling pathway / platelet aggregation / SH3 domain binding / peptidyl-tyrosine phosphorylation / specific granule lumen / Interferon gamma signaling / MAPK cascade / Interferon alpha/beta signaling / cell-cell junction / tertiary granule lumen / mitotic cell cycle / T cell receptor signaling pathway / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / intracellular signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / nucleolus / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / 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, non-receptor type-6, -11 / 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 / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsYang, J. / Cheng, Z. / Niu, Z. / Zhao, Z.J. / Zhou, G.W.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structural basis for substrate specificity of protein-tyrosine phosphatase SHP-1.
Authors: Yang, J. / Cheng, Z. / Niu, T. / Liang, X. / Zhao, Z.J. / Zhou, G.W.
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE 1C
B: PEPTIDE PY469


Theoretical massNumber of molelcules
Total (without water)33,7942
Polymers33,7942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area14080 Å2
MethodPISA
2
A: PROTEIN-TYROSINE PHOSPHATASE 1C
B: PEPTIDE PY469

A: PROTEIN-TYROSINE PHOSPHATASE 1C
B: PEPTIDE PY469


Theoretical massNumber of molelcules
Total (without water)67,5884
Polymers67,5884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6290 Å2
ΔGint-35 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.58, 45.21, 56.27
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE 1C / PTP-1C / HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE / SH-PTP1


Mass: 32558.781 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: C455S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Protein/peptide PEPTIDE PY469


Mass: 1235.146 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide occurs naturally in humans (Homo sapiens)

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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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
21.9 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / % possible obs: 85 % / Rmerge(I) obs: 0.097
Reflection
*PLUS
Num. obs: 8998 / % possible obs: 85 % / Num. measured all: 27345

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 2.5→6 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.303 844 Random
Rwork0.194 --
obs0.199 7199 -
all-8433 -
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 0 0 2374
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg27.6
X-RAY DIFFRACTIONx_torsion_impr_deg0.6
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor all: 0.199 / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4

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