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- PDB-3sr9: Crystal structure of mouse PTPsigma -

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Basic information

Entry
Database: PDB / ID: 3sr9
TitleCrystal structure of mouse PTPsigma
ComponentsReceptor-type tyrosine-protein phosphatase S
KeywordsHYDROLASE / tyrosine phosphatase
Function / homology
Function and homology information


negative regulation of toll-like receptor 9 signaling pathway / : / : / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / negative regulation of interferon-alpha production / : / chondroitin sulfate binding / negative regulation of collateral sprouting / negative regulation of axon regeneration ...negative regulation of toll-like receptor 9 signaling pathway / : / : / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / negative regulation of interferon-alpha production / : / chondroitin sulfate binding / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development / synaptic membrane adhesion / regulation of postsynaptic density assembly / negative regulation of axon extension / corpus callosum development / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / spinal cord development / phosphoprotein phosphatase activity / regulation of presynapse assembly / peptidyl-tyrosine dephosphorylation / cerebellum development / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampus development / synapse organization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / cerebral cortex development / negative regulation of neuron projection development / heparin binding / growth cone / perikaryon / axon / glutamatergic synapse / plasma membrane / cytosol
Similarity search - Function
Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set 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 superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase S
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, J. / Hou, L. / Li, J. / Ding, J.
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2011
Title: Structural insights into the homology and differences between mouse protein tyrosine phosphatase-sigma and human protein tyrosine phosphatase-sigma
Authors: Hou, L. / Wang, J. / Zhou, Y. / Li, J. / Zang, Y. / Li, J.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase S


Theoretical massNumber of molelcules
Total (without water)67,2071
Polymers67,2071
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.653, 94.653, 124.201
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase S / R-PTP-S / PTPNU-3 / Receptor-type tyrosine-protein phosphatase sigma / R-PTP-sigma


Mass: 67207.094 Da / Num. of mol.: 1 / Fragment: UNP residues 1326-1901
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprs / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLys / References: UniProt: B0V2N1, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 15% polyethylene glycol 3350, 0.08M malic acid, pH 7.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22320

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FH7

2fh7


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.24 / Cross valid method: THROUGHOUT / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 1117 5 %RANDOM
Rwork0.2327 ---
obs0.2347 21203 90.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 150.37 Å2 / Biso mean: 62.5058 Å2 / Biso min: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 0 89 4686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224711
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.9436384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23523.5240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22415795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8931539
X-RAY DIFFRACTIONr_chiral_restr0.0650.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213657
X-RAY DIFFRACTIONr_mcbond_it1.0611.52831
X-RAY DIFFRACTIONr_mcangle_it1.95124591
X-RAY DIFFRACTIONr_scbond_it1.28331880
X-RAY DIFFRACTIONr_scangle_it2.3574.51793
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 88 -
Rwork0.295 1576 -
all-1664 -
obs--92.6 %

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