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- PDB-5mk0: Crystal structure of the His Domain Protein Tyrosine Phosphatase ... -

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Basic information

Entry
Database: PDB / ID: 5mk0
TitleCrystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Endofin peptide complex)
Components
  • Tyrosine-protein phosphatase non-receptor type 23
  • Zinc finger FYVE domain-containing protein 16
KeywordsHYDROLASE / ESCRT-III Endofin
Function / homology
Function and homology information


positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / 1-phosphatidylinositol binding / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / vesicle organization / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to lysosome / Signaling by BMP ...positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / 1-phosphatidylinositol binding / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / vesicle organization / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to lysosome / Signaling by BMP / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Interleukin-37 signaling / endocytic recycling / endosomal transport / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of endocytosis / cilium assembly / protein-tyrosine-phosphatase / ciliary basal body / protein tyrosine phosphatase activity / early endosome membrane / early endosome / nuclear body / endosome / intracellular membrane-bounded organelle / protein kinase binding / signal transduction / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / alix/aip1 like domains / ALIX V-shaped domain / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily ...Domain of unknown function DUF3480 / Zinc finger FYVE domain containing protein, SARA/endofin / Smad anchor for receptor activation-like, C-terminal / Domain of unknown function (DUF3480) / alix/aip1 like domains / ALIX V-shaped domain / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Zinc finger, FYVE/PHD-type / Alpha Horseshoe / Zinc finger, RING/FYVE/PHD-type / Mainly Alpha
Similarity search - Domain/homology
Zinc finger FYVE domain-containing protein 16 / Tyrosine-protein phosphatase non-receptor type 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.765 Å
AuthorsLevy, C. / Gahloth, D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K011049/1 United Kingdom
Medical Research Council (United Kingdom)G0701140 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K008773/1 United Kingdom
CitationJournal: Structure / Year: 2017
Title: Structural Basis for Specific Interaction of TGF beta Signaling Regulators SARA/Endofin with HD-PTP.
Authors: Gahloth, D. / Levy, C. / Walker, L. / Wunderley, L. / Mould, A.P. / Taylor, S. / Woodman, P. / Tabernero, L.
History
DepositionDec 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 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: Tyrosine-protein phosphatase non-receptor type 23
B: Zinc finger FYVE domain-containing protein 16
C: Tyrosine-protein phosphatase non-receptor type 23
D: Zinc finger FYVE domain-containing protein 16


Theoretical massNumber of molelcules
Total (without water)86,5734
Polymers86,5734
Non-polymers00
Water9,080504
1
A: Tyrosine-protein phosphatase non-receptor type 23
B: Zinc finger FYVE domain-containing protein 16


Theoretical massNumber of molelcules
Total (without water)43,2872
Polymers43,2872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-13 kcal/mol
Surface area17530 Å2
MethodPISA
2
C: Tyrosine-protein phosphatase non-receptor type 23
D: Zinc finger FYVE domain-containing protein 16


Theoretical massNumber of molelcules
Total (without water)43,2872
Polymers43,2872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-7 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.751, 64.690, 70.621
Angle α, β, γ (deg.)101.39, 97.16, 102.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 23 / His domain-containing protein tyrosine phosphatase / HD-PTP / Protein tyrosine phosphatase TD14 / PTP-TD14


Mass: 40719.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN23, KIAA1471 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3S7, protein-tyrosine-phosphatase
#2: Protein/peptide Zinc finger FYVE domain-containing protein 16 / Endofin / Endosome-associated FYVE domain protein


Mass: 2566.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z3T8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium tartrate dibasic, 20% PEG3350 and 0.1 M MMT buffer pH 9.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.765→41.19 Å / Num. obs: 69302 / % possible obs: 96.48 % / Redundancy: 2.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.0544 / Net I/σ(I): 10.2
Reflection shellResolution: 1.765→1.828 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.23 / CC1/2: 0.975 / % possible all: 93.55

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Processing

Software
NameVersionClassification
PHENIX(1.11_2563: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RAU

3rau


Resolution: 1.765→41.19 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 20.42
RfactorNum. reflection% reflection
Rfree0.1929 1982 2.86 %
Rwork0.1601 --
obs0.1611 69278 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.765→41.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5967 0 0 504 6471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056149
X-RAY DIFFRACTIONf_angle_d0.6348309
X-RAY DIFFRACTIONf_dihedral_angle_d11.1323759
X-RAY DIFFRACTIONf_chiral_restr0.042902
X-RAY DIFFRACTIONf_plane_restr0.0041083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7654-1.80950.29641340.25624638X-RAY DIFFRACTION93
1.8095-1.85840.29291410.23154759X-RAY DIFFRACTION95
1.8584-1.91310.25131400.21354758X-RAY DIFFRACTION96
1.9131-1.97490.24061410.20294743X-RAY DIFFRACTION96
1.9749-2.04550.24161410.18454807X-RAY DIFFRACTION96
2.0455-2.12740.21961430.16884839X-RAY DIFFRACTION97
2.1274-2.22420.18361420.15224791X-RAY DIFFRACTION97
2.2242-2.34140.17541400.1454843X-RAY DIFFRACTION97
2.3414-2.48810.19121440.14754839X-RAY DIFFRACTION97
2.4881-2.68020.17211430.14854848X-RAY DIFFRACTION97
2.6802-2.94990.16381410.1584861X-RAY DIFFRACTION97
2.9499-3.37650.1841430.16084839X-RAY DIFFRACTION97
3.3765-4.25340.18091430.13834861X-RAY DIFFRACTION98
4.2534-41.190.18271460.15434870X-RAY DIFFRACTION98

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