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- PDB-6suc: Human PTPRU D1 domain, oxidised form -

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Basic information

Entry
Database: PDB / ID: 6suc
TitleHuman PTPRU D1 domain, oxidised form
ComponentsReceptor-type tyrosine-protein phosphatase U
KeywordsHYDROLASE / Phosphatase / Receptor / Pseudophosphatase / redox
Function / homology
Function and homology information


cell surface receptor protein tyrosine phosphatase signaling pathway / positive regulation of cell-cell adhesion mediated by cadherin / homotypic cell-cell adhesion / transmembrane receptor protein tyrosine phosphatase activity / protein localization to cell surface / animal organ regeneration / response to glucocorticoid / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of cell migration ...cell surface receptor protein tyrosine phosphatase signaling pathway / positive regulation of cell-cell adhesion mediated by cadherin / homotypic cell-cell adhesion / transmembrane receptor protein tyrosine phosphatase activity / protein localization to cell surface / animal organ regeneration / response to glucocorticoid / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of cell migration / protein tyrosine phosphatase activity / negative regulation of canonical Wnt signaling pathway / Signaling by SCF-KIT / beta-catenin binding / cell-cell junction / cell differentiation / cell adhesion / negative regulation of cell population proliferation / plasma membrane
Similarity search - Function
: / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain ...: / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase U
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsHay, I.M. / Fearnley, G.W. / Sharpe, H.J. / Deane, J.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Royal SocietyUF150682 United Kingdom
Wellcome Trust109407 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: The receptor PTPRU is a redox sensitive pseudophosphatase.
Authors: Hay, I.M. / Fearnley, G.W. / Rios, P. / Kohn, M. / Sharpe, H.J. / Deane, J.E.
History
DepositionSep 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase U


Theoretical massNumber of molelcules
Total (without water)34,0271
Polymers34,0271
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.090, 107.920, 89.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1240-

HOH

21A-1290-

HOH

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase U / R-PTP-U / Pancreatic carcinoma phosphatase 2 / PCP-2 / Protein-tyrosine phosphatase J / hPTP-J / ...R-PTP-U / Pancreatic carcinoma phosphatase 2 / PCP-2 / Protein-tyrosine phosphatase J / hPTP-J / Protein-tyrosine phosphatase pi / PTP pi / Protein-tyrosine phosphatase receptor omicron / PTP-RO / Receptor-type protein-tyrosine phosphatase psi / R-PTP-psi


Mass: 34026.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRU, FMI, PCP2, PTPRO / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q92729, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BICINE, pH 9, 1 M lithium chloride, 20% (w/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.97→89.28 Å / Num. obs: 21600 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 31.48 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.055 / Net I/σ(I): 9
Reflection shellResolution: 1.97→2 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1071 / CC1/2: 0.527 / Rpim(I) all: 0.458 / % possible all: 100

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Processing

Software
NameVersionClassification
DIALSdata collection
PHENIX1.16_3549refinement
Cootmodel building
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SUB

6sub


Resolution: 1.97→46.19 Å / SU ML: 0.2359 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2203
RfactorNum. reflection% reflection
Rfree0.2452 1022 4.74 %
Rwork0.2139 --
obs0.2154 21577 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.35 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 0 94 2022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512007
X-RAY DIFFRACTIONf_angle_d0.86272725
X-RAY DIFFRACTIONf_chiral_restr0.0537297
X-RAY DIFFRACTIONf_plane_restr0.0056344
X-RAY DIFFRACTIONf_dihedral_angle_d12.74881190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.070.33471320.26242903X-RAY DIFFRACTION99.93
2.07-2.20.24821360.22062893X-RAY DIFFRACTION99.93
2.2-2.370.23211610.2062891X-RAY DIFFRACTION100
2.37-2.610.26571370.2012922X-RAY DIFFRACTION100
2.61-2.990.25061500.20752937X-RAY DIFFRACTION99.97
2.99-3.770.22621340.20582958X-RAY DIFFRACTION99.9
3.77-46.190.24171720.21873051X-RAY DIFFRACTION99.81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.95380355099-0.8438308255490.5320142130461.00572710121-0.6533900781650.6945552714150.1292915760770.154555512798-0.142224218805-0.301705958445-0.126289291748-0.1393639896990.3073726796730.236615692349-0.06443050436660.2953700812280.0318748450976-0.01590508436940.251599550995-0.02748862374480.21914801923415.164351534512.848138168327.0712846017
20.700262103185-0.4962125383290.8099806058112.13143957485-0.4572849182860.94711640198-0.053352488865-0.1362191747340.03343490396380.08090604216910.0791399584551-0.198437642611-0.1243022440280.0251762860341-0.05734402050560.2112045071960.02431835858930.009560391778840.245419501909-0.02262112608750.21731255608810.012081259634.797540097136.3330460938
31.26659976176-1.379066759710.2671720123322.948886206620.3057009037530.819237965320.117564451004-0.0549500152773-0.0677017413054-0.133945733508-0.015851343525-0.03266184678380.221556392632-0.0582697146636-0.09232705023140.218987826975-0.00281685389243-0.03585497711820.241598318580.01550677634310.24064871724313.648192937713.73421357236.3290395699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 872 through 957 )
2X-RAY DIFFRACTION2chain 'A' and (resid 958 through 1048 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1049 through 1147 )

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