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- PDB-2yd2: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -

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Basic information

Entry
Database: PDB / ID: 2yd2
TitleCrystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Sigma
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / establishment of endothelial intestinal barrier ...negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / establishment of endothelial intestinal barrier / synaptic membrane adhesion / negative regulation of axon extension / corpus callosum development / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / spinal cord development / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / ECM proteoglycans / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cerebellum development / hippocampus development / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / heparin binding / negative regulation of neuron projection development / presynaptic membrane / growth cone / perikaryon / axon / glutamatergic synapse / signal transduction / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
: / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...: / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Receptor-type tyrosine-protein phosphatase S
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsColes, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R.
CitationJournal: Science / Year: 2011
Title: Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension.
Authors: Coles, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R.
History
DepositionMar 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3258
Polymers23,7111
Non-polymers6147
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.400, 29.490, 61.580
Angle α, β, γ (deg.)90.00, 92.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S / PROTEIN TYROSINE PHOSPHATASE SIGMA / R-PTP-S / RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE SIGMA / R- ...PROTEIN TYROSINE PHOSPHATASE SIGMA / R-PTP-S / RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE SIGMA / R-PTP-SIGMA / RPTPS


Mass: 23710.613 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 30-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q13332, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE THREE N-TERMINAL AMINO ACID RESIDUES (ETG) AND NINE C- TERMINAL RESIDUES (GTKHHHHHH) DERIVE ...THE THREE N-TERMINAL AMINO ACID RESIDUES (ETG) AND NINE C- TERMINAL RESIDUES (GTKHHHHHH) DERIVE FROM THE PHLSEC VECTOR. THIS IS ISOFORM 2, Q13332-6.

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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: 2.38 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.2 / Details: 0.2M AMMONIUM IODIDE, 20% W/V PEG 3350, PH 6.2 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ASDC QUANTUM 4R / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.55→29 Å / Num. obs: 7438 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7
Reflection shellResolution: 2.55→2.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.6 / % possible all: 84.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
XDSdata reduction
xia2data scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YD4

2yd4


Resolution: 2.552→27.237 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 322 4.8 %
Rwork0.1962 --
obs0.1995 6759 89.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.183 Å2-0 Å2-4.5739 Å2
2---3.4048 Å20 Å2
3----6.4729 Å2
Refinement stepCycle: LAST / Resolution: 2.552→27.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 7 30 1561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061556
X-RAY DIFFRACTIONf_angle_d0.9052107
X-RAY DIFFRACTIONf_dihedral_angle_d13.321596
X-RAY DIFFRACTIONf_chiral_restr0.061232
X-RAY DIFFRACTIONf_plane_restr0.003283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5517-3.2140.2921220.2392954X-RAY DIFFRACTION82
3.214-27.23870.24942000.1773483X-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)
10.00850.002-0.01440.04420.00810.04340.0093-0.04120.008-0.008-0.0033-0.0063-0.0154-0.0009-0.00040.0375-0.00970.00880.045-0.00280.016-9.00255.8322-10.4816
20.01680.0096-0.02580.0135-0.00710.0677-0.01160.0065-0.00460.0088-0.0157-0.02540.0195-0.0263-0.08240.029-0.0141-0.00970.03360.00160.061-19.8205-4.2688-24.5624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 30:117)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 118:226)

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