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- PDB-3pxh: Tandem Ig domains of tyrosine phosphatase LAR -

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Basic information

Entry
Database: PDB / ID: 3pxh
TitleTandem Ig domains of tyrosine phosphatase LAR
ComponentsReceptor-type tyrosine-protein phosphatase F
KeywordsHYDROLASE / Ig domains / Cell adhesion / 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 / negative regulation of neurotrophin TRK receptor signaling pathway / neuron projection regeneration / Insulin receptor recycling / 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 / negative regulation of neurotrophin TRK receptor signaling pathway / neuron projection regeneration / Insulin receptor recycling / 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 / regulation of neuron projection development / negative regulation of epidermal growth factor receptor signaling pathway / phosphate ion binding / homophilic cell adhesion via plasma membrane adhesion molecules / phosphoprotein phosphatase activity / excitatory synapse / peptidyl-tyrosine dephosphorylation / cell adhesion molecule binding / negative regulation of insulin receptor signaling pathway / 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 / nervous system development / heparin binding / 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 / PTP type protein phosphatase domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / 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 / PTP type protein phosphatase domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / 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 F
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0009 Å
AuthorsBiersmith, B.H. / Bouyain, S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Immunoglobulin-like Domains 1 and 2 of the Protein Tyrosine Phosphatase LAR Adopt an Unusual Horseshoe-like Conformation.
Authors: Biersmith, B.H. / Hammel, M. / Geisbrecht, E.R. / Bouyain, S.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8153
Polymers21,6231
Non-polymers1922
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.450, 77.450, 68.499
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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


Mass: 21623.268 Da / Num. of mol.: 1 / Fragment: Ig domains 1 and 2 (UNP Residues 30-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprf, Lar / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2(DE3) / References: UniProt: A2A8L5, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% (w/v) PEG 1500, 50 mM citrate 5.5, 200 mM lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97242 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2010
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 15225 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Redundancy: 15.4 % / Rmerge(I) obs: 0.069 / Χ2: 0.979 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.078.70.36410661.0665.4
2.07-2.159.60.30912120.96574.8
2.15-2.2511.10.26914390.9589.5
2.25-2.3713.80.26315670.93797.5
2.37-2.5217.20.21616420.92899.8
2.52-2.7118.10.1616140.92199.9
2.71-2.9918.20.11116400.95999.8
2.99-3.42180.07816541.0199.9
3.42-4.3117.90.0616641.086100
4.31-50170.04517270.99399.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES IFHG AND 2IEP

2iep


Resolution: 2.0009→33.537 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7315 / SU ML: 0.26 / σ(F): 0 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 721 4.98 %RANDOM
Rwork0.2203 ---
obs0.2214 14492 88.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.987 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 171.77 Å2 / Biso mean: 53.4528 Å2 / Biso min: 20.01 Å2
Baniso -1Baniso -2Baniso -3
1-6.8297 Å20 Å2-0 Å2
2--6.8297 Å20 Å2
3----13.6594 Å2
Refinement stepCycle: LAST / Resolution: 2.0009→33.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 10 85 1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.031531
X-RAY DIFFRACTIONf_angle_d1.6742070
X-RAY DIFFRACTIONf_chiral_restr0.138228
X-RAY DIFFRACTIONf_plane_restr0.008274
X-RAY DIFFRACTIONf_dihedral_angle_d20.393577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0009-2.15540.3424910.3251856194760
2.1554-2.37230.34751300.29272572270284
2.3723-2.71540.35281600.28043022318297
2.7154-3.42060.24381670.24331143281100
3.4206-33.54150.19091730.178232073380100
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)
10.32610.344-0.35070.72570.04330.84450.1676-0.0349-0.02130.3915-0.1137-0.03790.1008-0.0435-0.04120.2158-0.0451-0.01240.1674-0.00750.084141.73430.909625.9309
20.3263-0.0852-0.28430.13520.14531.2483-0.06710.23720.02770.0849-0.08630.0637-0.2097-0.54490.070.23490.09670.04130.39830.02760.200624.298139.000816.8879
32.00051.99922.00042.00041.99972.00040.0437-0.85853.7468-0.75330.3162.70570.88730.4468-0.35050.81220.04360.06130.41470.01990.789240.538315.502917.1702
40.2143-0.0999-0.31390.24360.19750.6831-0.0460.0816-0.06550.1533-0.0173-0.0195-0.0748-0.23120.07670.2912-0.00160.02560.2951-0.00760.201635.63133.147423.906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 30:128A30 - 128
2X-RAY DIFFRACTION2chain A and resid 129:226A129 - 226
3X-RAY DIFFRACTION3chain BA1 - 2
4X-RAY DIFFRACTION4chain SA1 - 289

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