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- PDB-4yfe: Crystal structure of PTP delta Fn1-Fn2 -

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Basic information

Entry
Database: PDB / ID: 4yfe
TitleCrystal structure of PTP delta Fn1-Fn2
ComponentsReceptor-type tyrosine-protein phosphatase delta
KeywordsHYDROLASE / synapse organizer
Function / homology
Function and homology information


Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis ...Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of immune response / dephosphorylation / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / neuron differentiation / presynaptic membrane / receptor complex / signaling receptor binding / glutamatergic synapse
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Immunoglobulin domain / 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 ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Immunoglobulin domain / 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 delta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 Å
AuthorsYamagata, A. / Fukai, S.
CitationJournal: Nat Commun / Year: 2015
Title: Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Authors: Yamagata, A. / Yoshida, T. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Iwasawa-Okamoto, S. / Mori, H. / Mishina, M. / Fukai, S.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Nov 8, 2023Group: 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 delta
B: Receptor-type tyrosine-protein phosphatase delta


Theoretical massNumber of molelcules
Total (without water)44,3492
Polymers44,3492
Non-polymers00
Water5,549308
1
A: Receptor-type tyrosine-protein phosphatase delta


Theoretical massNumber of molelcules
Total (without water)22,1751
Polymers22,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase delta


Theoretical massNumber of molelcules
Total (without water)22,1751
Polymers22,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.909, 65.081, 133.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase delta / R-PTP-delta


Mass: 22174.658 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 321-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q64487, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 3350, 0.1M MgCl2, 0.1M BisTris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 32731 / % possible obs: 99.8 % / Redundancy: 10.7 % / Rsym value: 0.118 / Net I/σ(I): 26.6
Reflection shellResolution: 1.97→2 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DJU, 2DLH

2dju

2dlh


Resolution: 1.972→48.404 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1660 5.07 %
Rwork0.2037 --
obs0.2048 32725 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.972→48.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 0 308 3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063064
X-RAY DIFFRACTIONf_angle_d1.3214202
X-RAY DIFFRACTIONf_dihedral_angle_d16.4851134
X-RAY DIFFRACTIONf_chiral_restr0.056482
X-RAY DIFFRACTIONf_plane_restr0.008548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9721-2.03010.26391320.23932512X-RAY DIFFRACTION99
2.0301-2.09560.29571250.23882566X-RAY DIFFRACTION100
2.0956-2.17050.26641450.22562550X-RAY DIFFRACTION100
2.1705-2.25740.2871500.2122535X-RAY DIFFRACTION100
2.2574-2.36020.22951190.21852569X-RAY DIFFRACTION100
2.3602-2.48460.24181280.21762574X-RAY DIFFRACTION100
2.4846-2.64020.26011330.22842549X-RAY DIFFRACTION100
2.6402-2.84410.26011370.21712595X-RAY DIFFRACTION100
2.8441-3.13020.22421390.21432604X-RAY DIFFRACTION100
3.1302-3.58310.20191480.19442604X-RAY DIFFRACTION100
3.5831-4.51380.18431280.17522653X-RAY DIFFRACTION100
4.5138-48.41840.18771760.18172754X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.5588 Å / Origin y: -6.1724 Å / Origin z: -2.6204 Å
111213212223313233
T-0.0551 Å2-0.0059 Å20.0282 Å2-0.1666 Å2-0.0697 Å2--0.0845 Å2
L-0.2604 °20.035 °20.2798 °2-0.4424 °20.2026 °2--0.7583 °2
S0.1192 Å °0.0141 Å °-0.0154 Å °-0.1214 Å °0.1161 Å °-0.0922 Å °-0.2554 Å °0.1809 Å °0.2471 Å °
Refinement TLS groupSelection details: all

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