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- PDB-9eey: STEP (PTPN5) with active-site disulfide bond and allosteric-site ... -

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Basic information

Entry
Database: PDB / ID: 9eey
TitleSTEP (PTPN5) with active-site disulfide bond and allosteric-site loop shift
ComponentsTyrosine-protein phosphatase non-receptor type 5
KeywordsHYDROLASE / STEP / PTPN5 / allostery / disulfide
Function / homology
Function and homology information


Interleukin-37 signaling / protein dephosphorylation / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm ...Interleukin-37 signaling / protein dephosphorylation / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / 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 ...Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGuerrero, L. / Ebrahim, A. / Riley, B.T. / Keedy, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133769 United States
Citation
Journal: Proteins / Year: 2025
Title: Three STEPs Forward: A Trio of Unexpected Structures of PTPN5.
Authors: Guerrero, L. / Ebrahim, A. / Riley, B.T. / Kim, S.H. / Bishop, A.C. / Wu, J. / Han, Y.N. / Tautz, L. / Keedy, D.A.
#1: Journal: Biorxiv / Year: 2025
Title: Three STEPs forward: A trio of unexpected structures of PTPN5.
Authors: Guerrero, L. / Ebrahim, A. / Riley, B.T. / Kim, S.H. / Bishop, A.C. / Wu, J. / Han, Y.N. / Tautz, L. / Keedy, D.A.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author / Item: _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 7, 2025Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Feb 4, 2026Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3973
Polymers35,2051
Non-polymers1922
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.673, 63.621, 135.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 5 / Neural-specific protein-tyrosine phosphatase / Striatum-enriched protein-tyrosine phosphatase / STEP


Mass: 35204.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54829, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 3350, 0.2 M lithium sulfate, 0.1 M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.75→63.62 Å / Num. obs: 35607 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 31.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.045 / Rrim(I) all: 0.164 / Net I/σ(I): 7.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11.2 % / Rmerge(I) obs: 4.668 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1726 / CC1/2: 0.32 / Rpim(I) all: 1.443 / Rrim(I) all: 4.89 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia23.7.1data reduction
DIALS3.7.1-gfb34cbf01-releasedata scaling
PHASER2.8.2 (svn 8393)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→57.61 Å / SU ML: 0.2572 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2377 1771 5 %
Rwork0.1988 33681 -
obs0.2008 35452 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.92 Å2
Refinement stepCycle: LAST / Resolution: 1.75→57.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 10 62 2277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01362286
X-RAY DIFFRACTIONf_angle_d0.99883106
X-RAY DIFFRACTIONf_chiral_restr0.0646338
X-RAY DIFFRACTIONf_plane_restr0.0085400
X-RAY DIFFRACTIONf_dihedral_angle_d13.0487854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.38881400.38062504X-RAY DIFFRACTION98.44
1.8-1.850.31141130.33492559X-RAY DIFFRACTION99.63
1.85-1.910.43381380.36552541X-RAY DIFFRACTION99.3
1.91-1.980.35311290.29552557X-RAY DIFFRACTION99.11
1.98-2.060.23171280.23592539X-RAY DIFFRACTION99.85
2.06-2.150.28921400.21812576X-RAY DIFFRACTION99.89
2.15-2.260.26261560.21652550X-RAY DIFFRACTION99.78
2.26-2.410.23881500.21872554X-RAY DIFFRACTION99.96
2.41-2.590.24861280.1832611X-RAY DIFFRACTION99.96
2.59-2.850.22741400.1932604X-RAY DIFFRACTION100
2.85-3.270.24411290.20532626X-RAY DIFFRACTION99.89
3.27-4.110.20761370.17482649X-RAY DIFFRACTION99.96
4.11-57.610.21681430.17592811X-RAY DIFFRACTION99.97

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