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- PDB-8slu: Crystal structure of human STEP (PTPN5) at cryogenic temperature ... -

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Basic information

Entry
Database: PDB / ID: 8slu
TitleCrystal structure of human STEP (PTPN5) at cryogenic temperature (100 K) and high pressure (205 MPa)
ComponentsTyrosine-protein phosphatase non-receptor type 5
KeywordsHYDROLASE / PTPN5 / STEP / Phosphatase
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 / Tyrosine specific protein phosphatases domain profile. / 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: 1.84 Å
AuthorsEbrahim, A. / Guerrero, L. / Riley, B.T. / Kim, M. / Huang, Q. / Finke, A.D. / Keedy, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133769 United States
CitationJournal: Biorxiv / Year: 2023
Title: Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase.
Authors: Guerrero, L. / Ebrahim, A. / Riley, B.T. / Kim, M. / Huang, Q. / Finke, A.D. / Keedy, D.A.
History
DepositionApr 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / struct_conf / struct_mon_prot_cis / symmetry
Item: _atom_sites.fract_transf_matrix[2][2] / _cell.volume ..._atom_sites.fract_transf_matrix[2][2] / _cell.volume / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _entity.pdbx_number_of_molecules / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _symmetry.space_group_name_Hall
Description: Atoms with unrealistic or zero occupancies
Details: Removed low/zero occupancy waters. Added a secondary conformation to the catalytic cysteine.
Provider: author / Type: Coordinate replacement

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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)32,8024
Polymers32,5181
Non-polymers2843
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.143, 63.466, 134.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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: 32517.986 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) / Strain (production host): Rosetta 2 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 52.01 % / Description: Rectangular
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.65
Details: 30% PEG 3350, 200 mM Li2SO4, 100 mM bis-tris pH 5.65

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationMonochromator: Dual bounce W/B4C multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.84→57.37 Å / Num. obs: 29880 / % possible obs: 99.46 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1138 / Rpim(I) all: 0.04787 / Rrim(I) all: 0.1237 / Net I/σ(I): 10.71
Reflection shellResolution: 1.84→1.906 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.127 / Mean I/σ(I) obs: 0.64 / Num. unique obs: 2949 / CC1/2: 0.687 / CC star: 0.903 / Rpim(I) all: 0.8879 / Rrim(I) all: 2.308 / % possible all: 99.12

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data scaling
DIMPLEv2.6.1data reduction
DIMPLEv2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→57.37 Å / SU ML: 0.281 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6952
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 1534 5.16 %
Rwork0.1948 28184 -
obs0.197 29718 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.64 Å2
Refinement stepCycle: LAST / Resolution: 1.84→57.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 16 98 2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242511
X-RAY DIFFRACTIONf_angle_d1.24083420
X-RAY DIFFRACTIONf_chiral_restr0.0615369
X-RAY DIFFRACTIONf_plane_restr0.0163449
X-RAY DIFFRACTIONf_dihedral_angle_d7.1612336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.90.39811240.37992523X-RAY DIFFRACTION99.14
1.9-1.970.38811360.32922525X-RAY DIFFRACTION98.59
1.97-2.050.29921190.27642515X-RAY DIFFRACTION99.06
2.05-2.140.30881430.24072507X-RAY DIFFRACTION99.59
2.14-2.250.27751480.2142528X-RAY DIFFRACTION99.59
2.25-2.390.26521440.19782526X-RAY DIFFRACTION99.66
2.39-2.580.22341520.1822552X-RAY DIFFRACTION99.71
2.58-2.840.24981300.18912565X-RAY DIFFRACTION99.74
2.84-3.250.23291300.18462616X-RAY DIFFRACTION100
3.25-4.090.18961490.162589X-RAY DIFFRACTION99.67
4.09-57.370.22431590.18362738X-RAY DIFFRACTION99.25

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