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- PDB-6x39: Crystal structure of the FN5 domain of Mouse Lar -

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Basic information

Entry
Database: PDB / ID: 6x39
TitleCrystal structure of the FN5 domain of Mouse Lar
ComponentsReceptor-type tyrosine-protein phosphatase F
KeywordsCELL ADHESION / Fibronectin type III / Receptor protein tyrosine phosphatase
Function / homology
Function and homology information


negative regulation of cell projection organization / negative regulation of cytokine-mediated signaling pathway / chondroitin sulfate proteoglycan binding / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / Insulin receptor recycling / neuron projection regeneration / negative regulation of neurotrophin TRK receptor signaling pathway / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity ...negative regulation of cell projection organization / negative regulation of cytokine-mediated signaling pathway / chondroitin sulfate proteoglycan binding / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / Insulin receptor recycling / neuron projection regeneration / negative regulation of neurotrophin TRK receptor signaling pathway / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / regulation of axon regeneration / regulation of synapse structure or activity / positive regulation of dendrite morphogenesis / regulation of postsynapse organization / negative regulation of epidermal growth factor receptor signaling pathway / regulation of neuron projection development / phosphate ion binding / homophilic cell adhesion via plasma membrane adhesion molecules / phosphoprotein phosphatase activity / excitatory synapse / peptidyl-tyrosine dephosphorylation / negative regulation of insulin receptor signaling pathway / cell adhesion molecule binding / protein-tyrosine-phosphatase / negative regulation of receptor binding / protein tyrosine phosphatase activity / postsynaptic density membrane / insulin receptor binding / receptor tyrosine kinase binding / positive regulation of neuron apoptotic process / cell migration / heparin binding / nervous system development / growth cone / endosome / neuron projection / positive regulation of apoptotic process / negative regulation of cell population proliferation / neuronal cell body / protein-containing complex binding
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
sorbitol / Receptor-type tyrosine-protein phosphatase F
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBouyain, S. / Kawakami, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R21AR066264 United States
CitationJournal: Plos One / Year: 2022
Title: Complex protein interactions mediate Drosophila Lar function in muscle tissue.
Authors: Kawakami, J. / Brooks, D. / Zalmai, R. / Hartson, S.D. / Bouyain, S. / Geisbrecht, E.R.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)11,7922
Polymers11,6101
Non-polymers1821
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.110, 86.110, 29.344
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1116-

HOH

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Components

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


Mass: 11610.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprf, Lar / Production host: Escherichia coli (E. coli) / References: UniProt: A2A8L5, protein-tyrosine-phosphatase
#2: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol / Sorbitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Na-cacodylate pH 6.5, 1.4 M Na-citrate tribasic dehydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 13907 / % possible obs: 99.5 % / Redundancy: 21.3 % / Biso Wilson estimate: 16.75 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 27.7
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1337

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Processing

Software
NameVersionClassification
PHENIX1.17_3644phasing
PHENIX1.17_3644refinement
HKL-2000data reduction
HKL-2000data scaling
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dlar FN5

Resolution: 1.7→28.19 Å / SU ML: 0.1435 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 1390 10.1 %
Rwork0.1637 12371 -
obs0.1663 13761 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 12 123 888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0107779
X-RAY DIFFRACTIONf_angle_d1.15451062
X-RAY DIFFRACTIONf_chiral_restr0.0758128
X-RAY DIFFRACTIONf_plane_restr0.0069135
X-RAY DIFFRACTIONf_dihedral_angle_d13.4023286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.22861270.191138X-RAY DIFFRACTION92.34
1.76-1.830.20641380.16851210X-RAY DIFFRACTION97.05
1.83-1.920.19771350.16611209X-RAY DIFFRACTION98.32
1.92-2.020.20881410.15091240X-RAY DIFFRACTION98.93
2.02-2.140.16851350.15981229X-RAY DIFFRACTION99.56
2.14-2.310.1861430.15271250X-RAY DIFFRACTION99.79
2.31-2.540.19941380.15471253X-RAY DIFFRACTION99.78
2.54-2.910.18711420.16661263X-RAY DIFFRACTION100
2.91-3.660.17681430.16011265X-RAY DIFFRACTION100
3.66-28.190.19211480.17171314X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 13.4523502714 Å / Origin y: 47.6505837211 Å / Origin z: 3.41369789875 Å
111213212223313233
T0.070881396696 Å20.0304533813127 Å2-0.0208023581496 Å2-0.151567064638 Å20.00456634406915 Å2--0.093533688701 Å2
L0.949748518083 °2-0.48962377987 °2-0.296404516075 °2-3.58062185054 °20.668697206167 °2--1.2651828351 °2
S0.0751156583688 Å °0.0322858551144 Å °0.101647024539 Å °0.0478598847748 Å °-0.106356205877 Å °-0.0208787580684 Å °-0.0798296207061 Å °0.0710545940695 Å °0.0281860006979 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 707 through 809)

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