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- PDB-6tpw: Crystal structures of FNIII domain one through four of the human ... -

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Basic information

Entry
Database: PDB / ID: 6tpw
TitleCrystal structures of FNIII domain one through 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 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7083
Polymers44,5161
Non-polymers1922
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-21 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.860, 74.860, 461.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 44516.367 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
#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.: 1 / 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: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 0.2 M Ammonium sulfate and 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→39.29 Å / Num. obs: 15285 / % possible obs: 98.7 % / Redundancy: 8.6 % / CC1/2: 0.999 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 1489 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TPV, 6TPU

6tpv

6tpu


Resolution: 2.9→38.985 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 40.65
RfactorNum. reflection% reflection
Rfree0.3012 751 4.97 %
Rwork0.2809 --
obs0.2821 15102 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 276.69 Å2 / Biso mean: 164.0143 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.9→38.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 10 1 2920
Biso mean--180.74 103.41 -
Num. residues----375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-3.12380.43441430.4166277798
3.1238-3.4380.37031470.335278298
3.438-3.93510.35611460.3111283999
3.9351-4.95620.30731520.2618288499
4.9562-38.9850.25251630.2554306999
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)
11.63160.55193.11384.99383.22036.95120.546-1.18290.1129-0.571-0.23330.5853-0.8112-0.6182-0.30932.3788-0.4205-0.13083.2233-0.21681.0356-41.7064-21.4442-111.7377
20.90180.4625-0.69691.1218-0.24671.1752-0.22040.6963-0.02210.07970.07730.168-0.0388-0.2712-0.08480.7018-0.04620.00683.02630.01720.7763-27.7406-3.0716-58.4703
32.1938-1.2403-2.3920.73191.36152.5907-0.18980.0922-0.88031.33690.28370.69310.53740.4226-0.04862.60980.36070.17472.70420.18960.9101-30.1077-13.9126-2.8242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 319 through 405 )A319 - 405
2X-RAY DIFFRACTION2chain 'A' and (resid 406 through 600 )A406 - 600
3X-RAY DIFFRACTION3chain 'A' and (resid 601 through 704 )A601 - 704

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