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- PDB-6d4d: Crystal structure of the PTP epsilon D1 domain -

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Basic information

Entry
Database: PDB / ID: 6d4d
TitleCrystal structure of the PTP epsilon D1 domain
ComponentsReceptor-type tyrosine-protein phosphatase epsilon
KeywordsHYDROLASE / phosphatase
Function / homology
Function and homology information


transmembrane receptor protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Receptor tyrosine-protein phosphatase, alpha/epsilon-type / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic 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 ...Receptor tyrosine-protein phosphatase, alpha/epsilon-type / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.765 Å
AuthorsLountos, G.T. / Raran-Kurussi, S. / Zhao, B.M. / Dyas, B.K. / Austin, B.P. / Burke Jr., T.R. / Ulrich, R.G. / Waugh, D.S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design.
Authors: Lountos, G.T. / Raran-Kurussi, S. / Zhao, B.M. / Dyas, B.K. / Burke Jr., T.R. / Ulrich, R.G. / Waugh, D.S.
History
DepositionApr 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase epsilon
B: Receptor-type tyrosine-protein phosphatase epsilon


Theoretical massNumber of molelcules
Total (without water)67,8322
Polymers67,8322
Non-polymers00
Water9,584532
1
A: Receptor-type tyrosine-protein phosphatase epsilon


Theoretical massNumber of molelcules
Total (without water)33,9161
Polymers33,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor-type tyrosine-protein phosphatase epsilon


Theoretical massNumber of molelcules
Total (without water)33,9161
Polymers33,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.055, 35.998, 115.023
Angle α, β, γ (deg.)90.00, 115.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-672-

HOH

21A-694-

HOH

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Components

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


Mass: 33915.930 Da / Num. of mol.: 2 / Fragment: epsilon D1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRE / Details (production host): pBA2525 / Production host: Escherichia coli (E. coli) / References: UniProt: P23469, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.2 M sodium chloride, 22% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 56107 / % possible obs: 98.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.9
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.542

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JJD

2jjd


Resolution: 1.765→38.282 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.48
RfactorNum. reflection% reflection
Rfree0.2223 1991 3.56 %
Rwork0.1782 --
obs0.1797 55924 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.765→38.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 0 532 5077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064703
X-RAY DIFFRACTIONf_angle_d0.816389
X-RAY DIFFRACTIONf_dihedral_angle_d4.7423923
X-RAY DIFFRACTIONf_chiral_restr0.053689
X-RAY DIFFRACTIONf_plane_restr0.005822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7646-1.80880.30581300.26563555X-RAY DIFFRACTION91
1.8088-1.85770.20991350.23013653X-RAY DIFFRACTION96
1.8577-1.91230.27621410.22413790X-RAY DIFFRACTION98
1.9123-1.9740.26061430.21053836X-RAY DIFFRACTION99
1.974-2.04460.24291400.19883837X-RAY DIFFRACTION99
2.0446-2.12650.24521450.19223876X-RAY DIFFRACTION99
2.1265-2.22320.2611400.18463866X-RAY DIFFRACTION100
2.2232-2.34040.25091430.18383857X-RAY DIFFRACTION100
2.3404-2.4870.24791420.18293881X-RAY DIFFRACTION100
2.487-2.6790.25521440.18733901X-RAY DIFFRACTION100
2.679-2.94850.23031460.18683923X-RAY DIFFRACTION100
2.9485-3.3750.19471440.16743919X-RAY DIFFRACTION100
3.375-4.25120.19251470.14643948X-RAY DIFFRACTION100
4.2512-38.29050.17651510.15614091X-RAY DIFFRACTION99

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