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- PDB-2yd8: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -

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Basic information

Entry
Database: PDB / ID: 2yd8
TitleCrystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase LAR in complex with sucrose octasulphate
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F
KeywordsHYDROLASE / RPTPF
Function / homology
Function and homology information


chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity ...chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / cell adhesion molecule binding / Insulin receptor recycling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of receptor binding / cell migration / heparin binding / cell adhesion / neuron projection / neuronal cell body / protein-containing complex binding / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
: / 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, 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
1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose / Receptor-type tyrosine-protein phosphatase F
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 18, 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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
Revision 2.2Nov 20, 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 F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8812
Polymers23,3801
Non-polymers5001
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.768, 78.768, 71.907
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F / LEUKOCYTE COMMON ANTIGEN RELATED / LAR / RECEPTOR PROTEIN TYROSINE PHOSPHATASE LAR


Mass: 23380.301 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 29-231
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: P10586, protein-tyrosine-phosphatase
#2: Sugar ChemComp-YYJ / 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose


Type: D-saccharide, beta linking / Mass: 500.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O18S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsSUCROSE OCTASULPHATE (SCR): THE SIX-MEMBERED RING OF SUCROSE OCTASULPHATE IS DISORDERED AND ...SUCROSE OCTASULPHATE (SCR): THE SIX-MEMBERED RING OF SUCROSE OCTASULPHATE IS DISORDERED AND THEREFORE ONLY THE FIVE-MEMBERED RING IS INCLUDED IN THE CRYSTAL STRUCTURE.
Sequence detailsTHE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES ...THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) DERIVE FROM THE PHLSEC VECTOR.

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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: 2.75 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M MES, 30% PEG 6000, PH 6.0 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 16614 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 32.14 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 10 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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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: 2.05→39.384 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 756 4.8 %
Rwork0.1949 --
obs0.1965 15755 95.11 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.675 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso mean: 46.34 Å2
Baniso -1Baniso -2Baniso -3
1-6.817 Å20 Å20 Å2
2--6.817 Å20 Å2
3----15.0394 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 28 96 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141564
X-RAY DIFFRACTIONf_angle_d1.2322123
X-RAY DIFFRACTIONf_dihedral_angle_d19.775621
X-RAY DIFFRACTIONf_chiral_restr0.078235
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0502-2.20840.331460.24972724X-RAY DIFFRACTION88
2.2084-2.43070.26771540.22372896X-RAY DIFFRACTION93
2.4307-2.78230.25251510.21212983X-RAY DIFFRACTION95
2.7823-3.50510.25211520.19983110X-RAY DIFFRACTION99
3.5051-39.39120.1881530.17513286X-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)
10.37060.4538-0.08960.40820.0980.5157-0.11850.03590.0528-0.04460.0788-0.07640.1922-0.0976-0.00010.24430.03860.01510.2561-0.01250.2212-33.226615.174515.3956
20.8460.04610.23950.8242-0.26910.84040.0732-0.36090.1519-0.0211-0.0124-0.1632-0.13520.54910.02140.1547-0.02510.01990.4955-0.0580.2783-16.522626.7975.4603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 30:129
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 130:227

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