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- PDB-2yd3: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -

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Basic information

Entry
Database: PDB / ID: 2yd3
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 / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development ...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 / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of axon extension / Synaptic adhesion-like molecules / corpus callosum development / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / spinal cord development / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / ECM proteoglycans / protein dephosphorylation / protein-tyrosine-phosphatase / cerebellum development / protein tyrosine phosphatase activity / hippocampus development / postsynaptic density membrane / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cerebral cortex development / synaptic vesicle membrane / negative regulation of neuron projection development / presynaptic membrane / heparin binding / growth cone / perikaryon / receptor complex / axon / glutamatergic synapse / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin domain / 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. ...Immunoglobulin domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase S
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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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)22,3253
Polymers22,2671
Non-polymers582
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.218, 104.218, 94.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2058-

HOH

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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: 22266.994 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 30-228
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) DERIVE FROM THE PHLSEC VECTOR. THIS RPTPSIGMA IG1-2 ...THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) DERIVE FROM THE PHLSEC VECTOR. THIS RPTPSIGMA IG1-2 CRYSTAL WAS OBTAINED AFTER PROTEOLYTIC CLEAVAGE OF RPTPSIGMA IG1-3 PROTEIN (TO RESIDUE 321, PLUS GTKHHHHHH). 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: 2.89 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.6 / Details: 0.2M SODIUM SULPHATE, 20% W/V PEG 3350, PH 6.6 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 12003 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 18.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YD4

2yd4


Resolution: 2.3→32.957 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 569 4.8 %
Rwork0.2007 --
obs0.2024 11897 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.599 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 38.77 Å2
Baniso -1Baniso -2Baniso -3
1--9.002 Å20 Å20 Å2
2---9.002 Å20 Å2
3---16.2234 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 2 82 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051578
X-RAY DIFFRACTIONf_angle_d0.8872136
X-RAY DIFFRACTIONf_dihedral_angle_d13.045605
X-RAY DIFFRACTIONf_chiral_restr0.055235
X-RAY DIFFRACTIONf_plane_restr0.003287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.53150.28691420.23612768X-RAY DIFFRACTION100
2.5315-2.89760.28341290.24512808X-RAY DIFFRACTION100
2.8976-3.64990.25761490.21712819X-RAY DIFFRACTION100
3.6499-32.960.19411490.16882933X-RAY DIFFRACTION100
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)
10.26350.0244-0.13630.5995-0.14210.1008-0.09480.1168-0.1924-0.0596-0.02070.01210.08570.0072-0.00110.19340.01870.00160.2194-0.03820.199335.17450.65084.9492
21.0053-0.2464-0.21890.03010.23540.71770.0532-0.1177-0.18260.0131-0.12150.09390.02980.0493-0.00080.1608-0.04490.03020.17660.00640.177220.84777.878820.9315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 29:129)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 130:228)

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