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- PDB-6uzt: Crystal Structure of RPTP alpha -

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Basic information

Entry
Database: PDB / ID: 6uzt
TitleCrystal Structure of RPTP alpha
ComponentsReceptor-type tyrosine-protein phosphatase alpha
KeywordsHYDROLASE / Protein tyrosine phosphatase / enzyme / alpha/beta protein / SIGNALING PROTEIN
Function / homology
Function and homology information


: / transmembrane receptor protein tyrosine phosphatase activity / regulation of focal adhesion assembly / plasma membrane => GO:0005886 / NCAM signaling for neurite out-growth / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / axon guidance ...: / transmembrane receptor protein tyrosine phosphatase activity / regulation of focal adhesion assembly / plasma membrane => GO:0005886 / NCAM signaling for neurite out-growth / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / axon guidance / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / MAPK cascade / insulin receptor signaling pathway / RAF/MAP kinase cascade / receptor complex / protein phosphorylation / focal adhesion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Receptor tyrosine-protein phosphatase alpha / 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 / 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 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSantelli, E. / Wen, Y. / Yang, S. / Svensson, M.N.D. / Stanford, S.M. / Bottini, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR066053 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: RPTP alpha phosphatase activity is allosterically regulated by the membrane-distal catalytic domain.
Authors: Wen, Y. / Yang, S. / Wakabayashi, K. / Svensson, M.N.D. / Stanford, S.M. / Santelli, E. / Bottini, N.
History
DepositionNov 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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 alpha
B: Receptor-type tyrosine-protein phosphatase alpha


Theoretical massNumber of molelcules
Total (without water)139,2202
Polymers139,2202
Non-polymers00
Water27,5451529
1
A: Receptor-type tyrosine-protein phosphatase alpha


Theoretical massNumber of molelcules
Total (without water)69,6101
Polymers69,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor-type tyrosine-protein phosphatase alpha


Theoretical massNumber of molelcules
Total (without water)69,6101
Polymers69,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.720, 112.110, 136.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-1143-

HOH

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Components

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


Mass: 69610.133 Da / Num. of mol.: 2 / Fragment: tandem catalytic domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRA, PTPA, PTPRL2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P18433, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1529 / 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: 2.88 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES, PEG 20000, DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 148737 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.037 / Rrim(I) all: 0.094 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.835.70.8774157372900.7510.4010.9661.9100
9.86-29.945.90.032592610020.9990.0140.03525.396.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.94 Å
Translation2.5 Å29.94 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.5.31data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFO

1yfo


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.8 / SU ML: 0.075 / SU R Cruickshank DPI: 0.0969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.191 7392 5 %RANDOM
Rwork0.155 ---
obs0.1568 141157 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 227.1 Å2 / Biso mean: 35.426 Å2 / Biso min: 15.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--1.59 Å20 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9420 0 0 1529 10949
Biso mean---45.91 -
Num. residues----1159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0139923
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179095
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.6513461
X-RAY DIFFRACTIONr_angle_other_deg1.3271.57521189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6951224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.11122.491574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69151801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9461571
X-RAY DIFFRACTIONr_chiral_restr0.0780.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0211136
X-RAY DIFFRACTIONr_gen_planes_other00.022133
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 545 -
Rwork0.261 10297 -
all-10842 -
obs--99.79 %
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)
10.954-0.03120.18450.6850.04830.99680.0066-0.06550.02630.1208-0.0231-0.0070.0258-0.0250.01650.02290.00430.0050.07950.04290.02784.62342.604151.41
21.19280.32830.11761.4749-0.38111.1387-0.02570.18150.0032-0.2570.0418-0.11340.22480.1543-0.0160.09650.02930.0290.0915-0.01670.0289-33.17122.963155.336
31.4497-0.1811-0.11951.54570.38361.0653-0.04080.0515-0.08320.07320.0484-0.00230.1165-0.129-0.00750.0567-0.0548-0.03940.08280.04840.04936.21427.686161.069
41.2970.0658-0.13320.8512-0.35091.8259-0.0404-0.0890.0370.07490.02960.0061-0.0228-0.19040.01070.05230.0427-0.0150.0919-0.03020.0119-37.41829.87190.452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A206 - 493
2X-RAY DIFFRACTION2B207 - 493
3X-RAY DIFFRACTION3A494 - 792
4X-RAY DIFFRACTION4B494 - 787

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