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- PDB-4hjq: SHP-1 catalytic domain WPD loop closed -

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Basic information

Entry
Database: PDB / ID: 4hjq
TitleSHP-1 catalytic domain WPD loop closed
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 / 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 / hematopoietic progenitor cell differentiation / Nuclear events stimulated by ALK signaling in cancer / 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
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8013 Å
AuthorsAlicea-Velazquez, N.L. / Boggon, T.J.
CitationJournal: Protein Pept.Lett. / Year: 2013
Title: SHP Family Protein Tyrosine Phosphatases Adopt Canonical Active-Site Conformations in the Apo and Phosphate-Bound States.
Authors: Alicea-Velazquez, N.L. / Boggon, T.J.
History
DepositionOct 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
B: Tyrosine-protein phosphatase non-receptor type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9324
Polymers70,7422
Non-polymers1902
Water12,286682
1
A: Tyrosine-protein phosphatase non-receptor type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4662
Polymers35,3711
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4662
Polymers35,3711
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.642, 57.783, 77.319
Angle α, β, γ (deg.)102.39, 94.71, 110.01
Int Tables number1
Space group name H-MP1

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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: 35370.824 Da / Num. of mol.: 2 / 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 (PTPN6) / 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.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH7.5, 20 mM MgCl2, 28% sodium polyacrylate 5100 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 21, 2011 / Details: Mirrors
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 66119 / Num. obs: 63496 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.053 / Net I/σ(I): 13.119
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.161 / Num. unique all: 6280 / Rsym value: 0.373 / % possible all: 95.4

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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: 1.8013→28.904 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 3216 5.07 %Random
Rwork0.1654 ---
obs0.1673 63489 96.1 %-
all-63489 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.932 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7161 Å2-0.1471 Å20.7945 Å2
2--4.2978 Å2-2.6218 Å2
3----2.5817 Å2
Refinement stepCycle: LAST / Resolution: 1.8013→28.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4528 0 10 682 5220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074773
X-RAY DIFFRACTIONf_angle_d1.0216500
X-RAY DIFFRACTIONf_dihedral_angle_d14.6841831
X-RAY DIFFRACTIONf_chiral_restr0.074696
X-RAY DIFFRACTIONf_plane_restr0.004854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8013-1.82820.34071290.27952305X-RAY DIFFRACTION85
1.8282-1.85670.28861460.25192557X-RAY DIFFRACTION96
1.8567-1.88720.27241440.21872623X-RAY DIFFRACTION95
1.8872-1.91970.24411510.19422589X-RAY DIFFRACTION96
1.9197-1.95460.18761420.18782599X-RAY DIFFRACTION96
1.9546-1.99220.24021250.18042677X-RAY DIFFRACTION97
1.9922-2.03280.21471200.17172588X-RAY DIFFRACTION96
2.0328-2.0770.21241470.1722687X-RAY DIFFRACTION96
2.077-2.12530.23251470.1622581X-RAY DIFFRACTION97
2.1253-2.17850.18761320.1652658X-RAY DIFFRACTION97
2.1785-2.23730.2181320.15662636X-RAY DIFFRACTION97
2.2373-2.30310.20941350.1592671X-RAY DIFFRACTION97
2.3031-2.37750.20241510.15922607X-RAY DIFFRACTION97
2.3775-2.46240.20471550.16112626X-RAY DIFFRACTION97
2.4624-2.56090.20731440.15952644X-RAY DIFFRACTION97
2.5609-2.67740.24581450.15862657X-RAY DIFFRACTION97
2.6774-2.81840.17661230.16052670X-RAY DIFFRACTION98
2.8184-2.99490.20061370.16222671X-RAY DIFFRACTION97
2.9949-3.22580.19461460.162643X-RAY DIFFRACTION97
3.2258-3.54990.16371390.15322674X-RAY DIFFRACTION97
3.5499-4.06240.19651570.14392639X-RAY DIFFRACTION98
4.0624-5.11360.15871430.13382646X-RAY DIFFRACTION97
5.1136-28.90790.19691260.19942625X-RAY DIFFRACTION96
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)
13.22512.38983.95983.16253.59446.061-0.1313-0.28320.29260.0468-0.24440.382-0.4481-0.65510.43120.22190.070.0540.24760.0260.1611-33.454542.89962.2924
20.82090.64360.15131.38440.39440.99580.06790.06530.0335-0.0138-0.00640.1117-0.2962-0.3281-0.0560.09840.03760.00730.09370.07160.1054-33.535737.163446.0986
30.85770.0120.03540.82860.82151.76620.02220.0347-0.0925-0.08090.2573-0.0637-0.1430.6495-0.05050.0416-0.03810.00450.01360.01740.0848-16.85733.041745.2139
43.5622-0.26320.26091.87550.05171.58890.0869-0.02970.63430.07690.1747-0.2855-0.74830.4090.01290.3119-0.08140.06310.1363-0.03220.1715-16.781748.872658.8519
52.0309-1.1301-1.88331.21521.16442.44130.04840.4996-0.1135-0.167-0.27270.20590.1006-0.54370.19560.1237-0.0043-0.02440.23420.00980.0947-29.638159.35517.4502
60.36260.38330.24821.35120.24791.0264-0.0618-0.1202-0.05320.1624-0.06390.14640.3269-0.21230.05150.1236-0.0320.00920.1010.01220.088-30.27156.290323.2238
71.2043-0.4548-0.39080.89091.11781.6191-0.0449-0.10.08360.05260.2096-0.11610.07750.3408-0.10070.07350.0121-0.00970.0991-0.01250.0926-13.4962.371223.3125
83.5682-0.0351-0.27482.19770.01421.7455-0.0179-0.0039-0.4588-0.01050.0822-0.23530.43670.2268-0.04920.18630.0311-0.01480.1082-0.01540.1008-13.940746.65979.238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 243:267)
2X-RAY DIFFRACTION2chain 'A' and (resseq 268:320)
3X-RAY DIFFRACTION3chain 'A' and (resseq 321:476)
4X-RAY DIFFRACTION4chain 'A' and (resseq 477:523)
5X-RAY DIFFRACTION5chain 'B' and (resseq 243:282)
6X-RAY DIFFRACTION6chain 'B' and (resseq 283:319)
7X-RAY DIFFRACTION7chain 'B' and (resseq 320:476)
8X-RAY DIFFRACTION8chain 'B' and (resseq 477:523)

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