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- PDB-4n5u: Crystal structure of the 4th FN3 domain of human Protein Tyrosine... -

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Basic information

Entry
Database: PDB / ID: 4n5u
TitleCrystal structure of the 4th FN3 domain of human Protein Tyrosine phosphatase, receptor type F [PSI-NYSGRC-006240]
ComponentsReceptor-type tyrosine-protein phosphatase F
KeywordsHYDROLASE / internal FN3 domain / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network / IFN
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
Receptor-type tyrosine-protein phosphatase F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.456 Å
AuthorsKumar, P.R. / Banu, R. / Bhosle, R. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S.J. ...Kumar, P.R. / Banu, R. / Bhosle, R. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S.J. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Attonito, J. / Love, J.D. / Patel, H. / Patel, R. / Seidel, R.D. / Smith, B. / Stead, M. / Toro, R. / Casadevall, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of the 4th FN3 domain of human PTP, receptor F [PSI-NYSGRC-006240]
Authors: Kumar, P.R. / Casadevall, A. / Almo, S.C.
History
DepositionOct 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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)13,0973
Polymers12,9051
Non-polymers1922
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.011, 39.677, 68.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

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


Mass: 12905.143 Da / Num. of mol.: 1 / Fragment: Fibronectin type-III 4 domain, residues 601-705
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAR, PTPRF / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: P10586, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.9 Å3/Da / Density % sol: 35.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol, Reservoir (0.2M Lithium Sulfate, 0.1M CAPS, 1.2M NaH2PO4/0.8M K2HPO4), Cryoprotection (2M Li2SO4), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.456→34.337 Å / Num. obs: 16720 / % possible obs: 94 % / Redundancy: 8.1 %

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Processing

Software
NameVersionClassificationNB
SCALA0.1.29data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
XDSdata reduction
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EDX

2edx


Resolution: 1.456→34.337 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 836 5.02 %
Rwork0.1623 --
obs0.1641 16660 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7118 Å2
Refinement stepCycle: LAST / Resolution: 1.456→34.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 10 116 958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009927
X-RAY DIFFRACTIONf_angle_d1.2331283
X-RAY DIFFRACTIONf_dihedral_angle_d13.452340
X-RAY DIFFRACTIONf_chiral_restr0.076138
X-RAY DIFFRACTIONf_plane_restr0.007173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4562-1.54750.29551070.24731850X-RAY DIFFRACTION68
1.5475-1.66690.27651340.21162601X-RAY DIFFRACTION93
1.6669-1.83470.21931560.17692763X-RAY DIFFRACTION100
1.8347-2.10010.20231300.15192825X-RAY DIFFRACTION100
2.1001-2.64580.18711550.15712827X-RAY DIFFRACTION100
2.6458-34.34610.18091540.15382958X-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)
12.3632-0.0403-0.5527.428-4.70135.5430.01670.0485-0.0087-0.15840.27560.41860.089-0.3562-0.31950.10160.00880.00610.1616-0.02610.0904-11.34851.819-6.696
21.17720.5974-1.75691.6779-2.31927.18590.0361-0.1826-0.00960.1267-0.1297-0.0911-0.18870.51610.12640.1266-0.0123-0.00790.1318-0.01580.1199-3.93533.2363-1.544
31.87260.6578-2.83342.158-3.05789.9604-0.1014-0.0306-0.05140.0574-0.0789-0.12340.52830.3220.19570.1832-0.01290.00460.1305-0.02930.1755-5.9408-7.2128-0.3616
41.16661.1498-0.91873.9131-2.02733.0391-0.04890.1042-0.05160.14510.17910.0688-0.045-0.3133-0.14080.0977-0.0070.00320.1436-0.01250.1059-9.9926-0.00221.2555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 602 through 633 )
2X-RAY DIFFRACTION2chain 'A' and (resid 634 through 664 )
3X-RAY DIFFRACTION3chain 'A' and (resid 665 through 677 )
4X-RAY DIFFRACTION4chain 'A' and (resid 678 through 709 )

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