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

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Basic information

Entry
Database: PDB / ID: 5mjz
TitleCrystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Apo structure)
ComponentsTyrosine-protein phosphatase non-receptor type 23
KeywordsHYDROLASE / ESCRT-III
Function / homology
Function and homology information


positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endocytic recycling / Interleukin-37 signaling ...positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endocytic recycling / Interleukin-37 signaling / cilium assembly / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / centriolar satellite / early endosome / endosome / nuclear body / ciliary basal body / intracellular membrane-bounded organelle / protein kinase binding / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
alix/aip1 like domains / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. ...alix/aip1 like domains / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.867 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: Tyrosine-protein phosphatase non-receptor type 23


Theoretical massNumber of molelcules
Total (without water)81,4402
Polymers81,4402
Non-polymers00
Water9,764542
1
A: Tyrosine-protein phosphatase non-receptor type 23


Theoretical massNumber of molelcules
Total (without water)40,7201
Polymers40,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 23


Theoretical massNumber of molelcules
Total (without water)40,7201
Polymers40,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.498, 64.999, 81.504
Angle α, β, γ (deg.)90.00, 91.29, 90.00
Int Tables number4
Space group name H-MP1211

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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 BL21(DE3) (bacteria) / References: UniProt: Q9H3S7, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Apo- HD-PTPBro1 crystals were obtained in 0.2M L-Na-Glutamate, 0.2M Alanine, 0.2M Glycine, 0.2M Lysine HCl, 0.2M Serine, 0.1 M Imidazole; MES monohydrate at pH 6.5 and 30% Ethylene glycol, PEG8K.
Temp details: Cold Room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.867→28.49 Å / Num. obs: 60112 / % possible obs: 99.34 % / Redundancy: 4.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1246 / Net I/σ(I): 9.24
Reflection shellResolution: 1.867→1.934 Å / Redundancy: 4 % / Rmerge(I) obs: 0.8821 / Mean I/σ(I) obs: 1.99 / CC1/2: 0.586 / % possible all: 97.25

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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: 1.867→28.49 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.51
RfactorNum. reflection% reflection
Rfree0.2161 2004 3.33 %
Rwork0.176 --
obs0.1773 60091 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.867→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 0 0 542 6216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055830
X-RAY DIFFRACTIONf_angle_d0.7047876
X-RAY DIFFRACTIONf_dihedral_angle_d13.9453566
X-RAY DIFFRACTIONf_chiral_restr0.042854
X-RAY DIFFRACTIONf_plane_restr0.0041024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.91320.32921350.30413940X-RAY DIFFRACTION95
1.9132-1.9650.29551480.25214128X-RAY DIFFRACTION99
1.965-2.02280.23191500.22624122X-RAY DIFFRACTION100
2.0228-2.0880.26161340.20724155X-RAY DIFFRACTION100
2.088-2.16260.23471340.19874173X-RAY DIFFRACTION100
2.1626-2.24920.23381520.18954120X-RAY DIFFRACTION100
2.2492-2.35150.20431380.17994136X-RAY DIFFRACTION100
2.3515-2.47540.22551470.16724165X-RAY DIFFRACTION99
2.4754-2.63040.18211380.15884161X-RAY DIFFRACTION100
2.6304-2.83340.19831460.16314175X-RAY DIFFRACTION100
2.8334-3.11820.18551480.16734175X-RAY DIFFRACTION100
3.1182-3.56880.20721490.16874183X-RAY DIFFRACTION100
3.5688-4.49370.19531440.14514194X-RAY DIFFRACTION100

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