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- PDB-4grz: Crystal structure of SHP1 catalytic domain with PO4 -

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Basic information

Entry
Database: PDB / ID: 4grz
TitleCrystal structure of SHP1 catalytic domain with PO4
ComponentsTyrosine-protein phosphatase non-receptor type 6
KeywordsHYDROLASE / Phosphatase domain
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 / negative regulation of B cell receptor signaling pathway / negative regulation of peptidyl-tyrosine phosphorylation / regulation of B cell differentiation / negative regulation of inflammatory response to wounding / epididymis development / CD27 signaling pathway / transmembrane receptor protein tyrosine phosphatase activity / phosphorylation-dependent protein binding ...negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / negative regulation of B cell receptor signaling pathway / negative regulation of peptidyl-tyrosine phosphorylation / regulation of B cell differentiation / negative regulation of inflammatory response to wounding / epididymis development / CD27 signaling pathway / transmembrane receptor protein tyrosine phosphatase activity / phosphorylation-dependent protein binding / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of neutrophil activation / alpha-beta T cell receptor complex / CD22 mediated BCR regulation / regulation of release of sequestered calcium ion into cytosol / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Regulation of T cell activation by CD28 family / Signal regulatory protein family interactions / platelet formation / megakaryocyte development / Regulation of KIT signaling / Signaling by ALK / natural killer cell mediated cytotoxicity / negative regulation of T cell receptor signaling pathway / Platelet sensitization by LDL / regulation of G1/S transition of mitotic cell cycle / regulation of type I interferon-mediated signaling pathway / PECAM1 interactions / negative regulation of interleukin-6 production / peptidyl-tyrosine dephosphorylation / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / negative regulation of tumor necrosis factor production / Co-inhibition by PD-1 / Interleukin receptor SHC signaling / negative regulation of MAPK cascade / Regulation of IFNG signaling / hematopoietic progenitor cell differentiation / regulation of ERK1 and ERK2 cascade / Growth hormone receptor signaling / negative regulation of T cell proliferation / Nuclear events stimulated by ALK signaling in cancer / T cell proliferation / cell adhesion molecule binding / GPVI-mediated activation cascade / protein dephosphorylation / T cell costimulation / non-membrane spanning protein tyrosine phosphatase activity / phosphotyrosine residue binding / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / SH2 domain binding / negative regulation of innate immune response / negative regulation of angiogenesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / T cell activation / B cell receptor signaling pathway / peptidyl-tyrosine phosphorylation / cytokine-mediated signaling pathway / SH3 domain binding / platelet aggregation / 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 / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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 ...: / 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
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3732 Å
AuthorsAlicea-Velazquez, N.L. / Jakoncic, J. / Boggon, T.J.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Structure-guided studies of the SHP-1/JAK1 interaction provide new insights into phosphatase catalytic domain substrate recognition.
Authors: Alicea-Velazquez, N.L. / Jakoncic, J. / Boggon, T.J.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0132
Polymers32,9181
Non-polymers951
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.141, 45.404, 44.679
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1021-

HOH

21A-1061-

HOH

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 6 / Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / ...Hematopoietic cell protein-tyrosine phosphatase / Protein-tyrosine phosphatase 1C / PTP-1C / Protein-tyrosine phosphatase SHP-1 / SH-PTP1


Mass: 32918.117 Da / Num. of mol.: 1 / Fragment: Phosphatase domain UNP Residues 242-528 / Mutation: C453S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCP, PTP1C, PTPN6, SHP-1 / Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P29350, protein-tyrosine-phosphatase
#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.: 391 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium phosphate, 12% PEG2000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 4, 2010 / Details: mirrors
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. all: 68145 / Num. obs: 68145 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.049 / Net I/σ(I): 28.906
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.824 / Num. unique all: 6135 / Rsym value: 0.257 / % possible all: 88.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FPR

1fpr


Resolution: 1.3732→39.594 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 3445 5.06 %random
Rwork0.1685 ---
obs0.1695 68085 98.89 %-
all-68085 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.806 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0614 Å2-0 Å2-0.4423 Å2
2---1.9815 Å2-0 Å2
3---1.9201 Å2
Refinement stepCycle: LAST / Resolution: 1.3732→39.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 5 391 2669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062445
X-RAY DIFFRACTIONf_angle_d1.0893338
X-RAY DIFFRACTIONf_dihedral_angle_d13.027961
X-RAY DIFFRACTIONf_chiral_restr0.072358
X-RAY DIFFRACTIONf_plane_restr0.005440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3732-1.39210.29651560.26982491X-RAY DIFFRACTION96
1.3921-1.41190.26321350.25532561X-RAY DIFFRACTION99
1.4119-1.4330.31241380.25542577X-RAY DIFFRACTION99
1.433-1.45540.25631400.24122595X-RAY DIFFRACTION100
1.4554-1.47930.22261280.19752590X-RAY DIFFRACTION99
1.4793-1.50480.23841400.20382557X-RAY DIFFRACTION100
1.5048-1.53210.18181390.16772607X-RAY DIFFRACTION100
1.5321-1.56160.17091440.16122604X-RAY DIFFRACTION100
1.5616-1.59350.20951270.15282633X-RAY DIFFRACTION100
1.5935-1.62810.19011520.15262557X-RAY DIFFRACTION100
1.6281-1.6660.15941360.14982614X-RAY DIFFRACTION100
1.666-1.70770.1961320.15092598X-RAY DIFFRACTION100
1.7077-1.75390.17751340.14312605X-RAY DIFFRACTION100
1.7539-1.80550.16651460.14812608X-RAY DIFFRACTION100
1.8055-1.86370.16091510.15512612X-RAY DIFFRACTION100
1.8637-1.93030.26611320.21582593X-RAY DIFFRACTION100
1.9303-2.00760.15791310.17122580X-RAY DIFFRACTION99
2.0076-2.0990.17931390.15232605X-RAY DIFFRACTION100
2.099-2.20970.17531360.16222632X-RAY DIFFRACTION100
2.2097-2.34810.20951330.18972468X-RAY DIFFRACTION94
2.3481-2.52930.15651300.15822626X-RAY DIFFRACTION100
2.5293-2.78380.19281380.16022642X-RAY DIFFRACTION100
2.7838-3.18650.1791400.16362642X-RAY DIFFRACTION100
3.1865-4.0140.17621150.15052371X-RAY DIFFRACTION89
4.014-39.61050.18551530.17022672X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.879-4.2122-1.11933.43860.35550.64360.1620.29310.6913-0.0504-0.1271-0.453-0.06770.1399-0.05640.1235-0.0285-0.02230.15070.01210.1753-8.292333.509916.0129
23.6877-0.5581-0.04782.9007-0.56823.0395-0.0523-0.09820.11470.18090.002-0.0075-0.0880.16370.04280.0810.00470.00530.0212-0.00620.0667-22.876833.152518.917
30.7260.4015-0.36511.2570.22371.1987-0.0280.3320.0809-0.2860.00390.1668-0.06410.03230.00630.11860.0166-0.0240.16230.01540.0682-23.044529.09647.4045
41.3217-0.11760.15541.461-0.03211.05870.0663-0.0346-0.24610.14310.03440.34910.0586-0.0377-0.09070.0841-0.00370.01420.08110.00940.1619-30.707816.565519.8907
50.9911-0.1334-0.09161.73770.26831.0150.05820.2152-0.1905-0.1891-0.05960.15380.09880.0046-0.03020.09290.0154-0.03480.1021-0.03270.0847-21.045913.632910.0381
61.296-0.2416-0.18023.36250.41241.51880.04530.3989-0.2233-0.3437-0.0395-0.20640.12710.2753-0.04250.1140.04020.01830.2453-0.05680.124-7.157115.7246.7392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 245:269)
2X-RAY DIFFRACTION2chain 'A' and (resseq 270:292)
3X-RAY DIFFRACTION3chain 'A' and (resseq 293:322)
4X-RAY DIFFRACTION4chain 'A' and (resseq 323:401)
5X-RAY DIFFRACTION5chain 'A' and (resseq 402:478)
6X-RAY DIFFRACTION6chain 'A' and (resseq 479:524)

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