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- PDB-2bij: Crystal structure of the human protein tyrosine phosphatase PTPN5... -

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Basic information

Entry
Database: PDB / ID: 2bij
TitleCrystal structure of the human protein tyrosine phosphatase PTPN5 (STEP, striatum enriched enriched Phosphatase)
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 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, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBarr, A.J. / Debreczeni, J.E. / Eswaran, J. / Smee, C. / Burgess, N. / Gileadi, O. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Knapp, S. / von Delft, F.
CitationJournal: Biochem. J. / Year: 2006
Title: Crystal structures and inhibitor identification for PTPN5, PTPRR and PTPN7: a family of human MAPK-specific protein tyrosine phosphatases.
Authors: Eswaran, J. / von Kries, J.P. / Marsden, B. / Longman, E. / Debreczeni, J.E. / Ugochukwu, E. / Turnbull, A. / Lee, W.H. / Knapp, S. / Barr, A.J.
History
DepositionJan 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)35,3012
Polymers35,2051
Non-polymers961
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.808, 64.318, 101.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE, NON-RECEPTOR TYPE 5 / HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5


Mass: 35204.844 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 258-539
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN / Plasmid: PLIC SGC / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES ASP 289, LEU 298, VAL 299 AND THR 517 ARE GIVEN AS VARIANTS IN THE SWISS-PROT ENTRY FOR ...RESIDUES ASP 289, LEU 298, VAL 299 AND THR 517 ARE GIVEN AS VARIANTS IN THE SWISS-PROT ENTRY FOR P54829. RESIDUES -23 TO -1 FORM PART OF A N-TERMINAL HIS-TAG USED FOR EXPRESSION

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growDetails: PROTEIN SOLUTION: 10 MG/ML PTPN5, 50 MM HEPES PH 7.5, 200 MM NACL, 10 MM DTT PRECIPITANT: 25% PEG3350, 0.2 M LI2SO4, 100 MM BIS-TR-S PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 2, 2004 / Details: MULTILAYER MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→39.74 Å / Num. obs: 20825 / % possible obs: 95 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.14
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.05 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JLN

1jln


Resolution: 2.05→54.23 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.811 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 380-382 ARE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1047 5.1 %RANDOM
Rwork0.212 ---
obs0.215 19570 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å20 Å20 Å2
2---1.34 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.05→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 5 103 2373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222335
X-RAY DIFFRACTIONr_bond_other_d0.0010.022072
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.953179
X-RAY DIFFRACTIONr_angle_other_deg0.83834821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3824.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93315384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1431514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined0.2140.2463
X-RAY DIFFRACTIONr_nbd_other0.1810.22091
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21128
X-RAY DIFFRACTIONr_nbtor_other0.0840.21348
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0220.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7721.51461
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24122318
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88931000
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9854.5861
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.445 70
Rwork0.389 1486
Refinement TLS params.Method: refined / Origin x: 17.3326 Å / Origin y: -9.1959 Å / Origin z: -10.9622 Å
111213212223313233
T-0.0653 Å2-0.0142 Å2-0.0098 Å2--0.0433 Å20.024 Å2---0.0399 Å2
L0.8989 °2-0.3432 °2-0.5071 °2-1.1249 °20.3928 °2--1.9192 °2
S-0.0565 Å °-0.0273 Å °-0.0653 Å °0.0742 Å °0.0448 Å °0.0954 Å °0.1127 Å °0.0193 Å °0.0117 Å °

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