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- PDB-6d3f: Crystal Structure of the PTP epsilon D2 domain -

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Basic information

Entry
Database: PDB / ID: 6d3f
TitleCrystal Structure of the PTP epsilon D2 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: 2.271 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 16, 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

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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)64,6682
Polymers64,6682
Non-polymers00
Water3,567198
1
A: Receptor-type tyrosine-protein phosphatase epsilon


Theoretical massNumber of molelcules
Total (without water)32,3341
Polymers32,3341
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)32,3341
Polymers32,3341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.337, 74.300, 75.725
Angle α, β, γ (deg.)90.00, 91.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32333.779 Da / Num. of mol.: 2 / Fragment: D2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRE / Plasmid: pSRK2607 / Production host: Escherichia coli (E. coli) / References: UniProt: P23469, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bicine/Trizma base pH 8.5, 0.03 mM diethylene glycol, 0.03 M triethylene glycol, 0.03 M tetraethylne glycol, 0.03 M pentaethylene glycol, 10% (w/v) polyethylene glycol 4000, 20% (v/v) glycerol

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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: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 28821 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 14
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JJD

2jjd


Resolution: 2.271→44.874 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.13
RfactorNum. reflection% reflection
Rfree0.2359 2016 7 %
Rwork0.1729 --
obs0.1773 28797 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.271→44.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 0 198 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084449
X-RAY DIFFRACTIONf_angle_d0.8646033
X-RAY DIFFRACTIONf_dihedral_angle_d13.772647
X-RAY DIFFRACTIONf_chiral_restr0.057668
X-RAY DIFFRACTIONf_plane_restr0.006779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2709-2.32770.28991320.20531779X-RAY DIFFRACTION92
2.3277-2.39060.27311420.21111902X-RAY DIFFRACTION100
2.3906-2.46090.29461480.21581931X-RAY DIFFRACTION100
2.4609-2.54040.28271370.21361895X-RAY DIFFRACTION100
2.5404-2.63120.30151470.20651904X-RAY DIFFRACTION100
2.6312-2.73650.33841470.20051922X-RAY DIFFRACTION100
2.7365-2.8610.26581560.20291897X-RAY DIFFRACTION100
2.861-3.01180.27381460.18631928X-RAY DIFFRACTION100
3.0118-3.20050.28061380.17641938X-RAY DIFFRACTION100
3.2005-3.44750.19971510.1651910X-RAY DIFFRACTION100
3.4475-3.79430.20761390.15591934X-RAY DIFFRACTION100
3.7943-4.34290.17381470.14141924X-RAY DIFFRACTION100
4.3429-5.47010.19931440.14161941X-RAY DIFFRACTION100
5.4701-44.88320.22311420.17381976X-RAY DIFFRACTION99

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