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- PDB-6tpv: Crystal structures of FNIII domain one and two of the human leuco... -

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Basic information

Entry
Database: PDB / ID: 6tpv
TitleCrystal structures of FNIII domain one and two 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 / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / Insulin receptor recycling ...chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / Insulin receptor recycling / cell adhesion molecule binding / protein-tyrosine-phosphatase / negative regulation of receptor binding / protein tyrosine phosphatase activity / cell migration / heparin binding / cell adhesion / neuron projection / neuronal cell body / protein-containing complex binding / extracellular exosome / plasma membrane
Similarity search - Function
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 ...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
IMIDAZOLE / Receptor-type tyrosine-protein phosphatase F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
B: Receptor-type tyrosine-protein phosphatase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5283
Polymers45,4592
Non-polymers691
Water6,125340
1
A: Receptor-type tyrosine-protein phosphatase F


Theoretical massNumber of molelcules
Total (without water)22,7291
Polymers22,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7982
Polymers22,7291
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.270, 50.843, 65.525
Angle α, β, γ (deg.)90.000, 97.220, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 22729.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRF, LAR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10586, protein-tyrosine-phosphatase
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 48.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M Sodium citrate tribasic dihydrate pH 8.3, 20 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→40.05 Å / Num. obs: 37701 / % possible obs: 97.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 17.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.81 / Num. unique obs: 2761 / CC1/2: 0.888 / Rrim(I) all: 0.98 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIXv1.16-3549-000refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DJU

2dju


Resolution: 1.8→40.05 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.22 --1992
Rwork0.1855 ---
obs-37545 97.44 %-
Displacement parametersBiso mean: 41.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 5 340 3300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01373072
X-RAY DIFFRACTIONf_angle_d1.18254217
X-RAY DIFFRACTIONf_chiral_restr0.0786468
X-RAY DIFFRACTIONf_plane_restr0.0089559
X-RAY DIFFRACTIONf_dihedral_angle_d21.87261849

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