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- PDB-6tpt: Crystal structures of FNIII domain three and four of the human le... -

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Basic information

Entry
Database: PDB / ID: 6tpt
TitleCrystal structures of FNIII domain three and four of the human leucocyte common antigen-related protein, LAR
ComponentsReceptor-type tyrosine-protein phosphatase F
KeywordsCELL ADHESION / Fibronectin type-III / adhesion protein
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
Receptor-type tyrosine-protein phosphatase F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsVilstrup, J.P. / Thirup, S.S. / Simonsen, A. / Birkefeldt, T. / Strandbygaard, D.
Funding support Denmark, 2items
OrganizationGrant numberCountry
LundbeckfondenR198-2015-168 Denmark
Novo Nordisk FoundationDFF 4183-00604 Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal and solution structures of fragments of the human leucocyte common antigen-related protein.
Authors: Vilstrup, J. / Simonsen, A. / Birkefeldt, T. / Strandbygard, D. / Lyngso, J. / Pedersen, J.S. / Thirup, S.
History
DepositionDec 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Receptor-type tyrosine-protein phosphatase F


Theoretical massNumber of molelcules
Total (without water)21,9021
Polymers21,9021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.750, 63.750, 236.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase F / Leukocyte common antigen related / LAR


Mass: 21902.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRF, LAR / Production host: Escherichia coli (E. coli) / References: UniProt: P10586, protein-tyrosine-phosphatase

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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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M Sodium fluoride, 0.1 M Bis-tris propane pH 6.5, and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→28 Å / Num. obs: 5225 / % possible obs: 99.3 % / Redundancy: 12.2 % / CC1/2: 0.998 / Net I/σ(I): 14.98
Reflection shellResolution: 3.2→3.3 Å / Num. unique obs: 493 / CC1/2: 0.937

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EDX

2edx


Resolution: 3.2→28 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.269 --
Rwork0.22 --
obs-5225 99.3 %
Displacement parametersBiso mean: 150.21 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 0 0 1534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00141576
X-RAY DIFFRACTIONf_angle_d0.4242157
X-RAY DIFFRACTIONf_chiral_restr0.0406237
X-RAY DIFFRACTIONf_plane_restr0.0036283
X-RAY DIFFRACTIONf_dihedral_angle_d14.5894578

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