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- PDB-8gwh: PTPN21 PTP domain C1108S mutant in complex with SRC pTyr530 peptide -

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Basic information

Entry
Database: PDB / ID: 8gwh
TitlePTPN21 PTP domain C1108S mutant in complex with SRC pTyr530 peptide
Components
  • SRC pTyr530 peptide
  • Tyrosine-protein phosphatase non-receptor type 21
KeywordsHYDROLASE / PTPN21 / phosphotase domain / PTP / PTPD1
Function / homology
Function and homology information


protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cytoskeleton / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. ...Protein-tyrosine phosphatase, non-receptor type-14/21 / PTPN14/21, FERM domain C-lobe / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, L. / Zheng, Y.Y. / Zhou, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2024
Title: Structural analysis of PTPN21 reveals a dominant-negative effect of the FERM domain on its phosphatase activity.
Authors: Chen, L. / Qian, Z. / Zheng, Y. / Zhang, J. / Sun, J. / Zhou, C. / Xiao, H.
History
DepositionSep 17, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 21
E: SRC pTyr530 peptide


Theoretical massNumber of molelcules
Total (without water)35,4082
Polymers35,4082
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-8 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.545, 104.545, 71.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 21 / Protein-tyrosine phosphatase D1


Mass: 34664.465 Da / Num. of mol.: 1 / Fragment: PTPN21 PTP domain / Mutation: C1108S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN21, PTPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16825, protein-tyrosine-phosphatase
#2: Protein/peptide SRC pTyr530 peptide


Mass: 743.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: sodium acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97875 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 2→46.75 Å / Num. obs: 51259 / % possible obs: 99.63 % / Redundancy: 14.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1188 / Rpim(I) all: 0.03277 / Net I/σ(I): 14.13
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.9286 / Num. unique obs: 2693 / CC1/2: 0.921 / Rpim(I) all: 0.2478

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BZL

2bzl


Resolution: 2→46.75 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 2497 4.87 %
Rwork0.181 48762 -
obs0.1824 51259 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.56 Å2 / Biso mean: 46.8635 Å2 / Biso min: 19.55 Å2
Refinement stepCycle: final / Resolution: 2→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 0 142 2570
Biso mean---47.96 -
Num. residues----299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.040.41411340.29226932827100
2.04-2.080.32981470.26122717286499
2.08-2.130.24281290.23162697282699
2.13-2.170.23821390.205926912830100
2.17-2.230.25761300.201127242854100
2.23-2.290.21971330.190926852818100
2.29-2.360.23741310.196227252856100
2.36-2.430.25541480.20232704285299
2.43-2.520.17971210.209827182839100
2.52-2.620.25211180.1927242842100
2.62-2.740.26781550.203627232878100
2.74-2.880.23851330.187927242857100
2.88-3.070.21821480.195726922840100
3.07-3.30.2371420.181927042846100
3.3-3.630.21511490.170627192868100
3.63-4.160.18481450.155926972842100
4.16-5.240.14751510.144727102861100
5.24-46.750.17581440.176227152859100
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)
12.296-0.0361-0.4371.51421.41213.9497-0.2042-0.1853-0.02310.17170.0496-0.14660.55590.89240.15740.26350.142-0.01230.27910.060.2752-9.534-31.00717.816
22.13240.1939-0.55192.83911.03714.7139-0.0910.136-0.204-0.0244-0.12250.15470.7763-0.20730.15750.3745-0.02460.01720.20810.00040.2758-20.309-37.9296.401
32.91560.0147-0.47612.49360.54884.6062-0.3008-0.2556-0.38260.40550.0404-0.09821.07320.22250.13620.46260.09570.06280.22980.01290.2606-17.854-36.13827.239
41.06121.8061-1.7383.7228-3.66353.65290.3043-0.29791.33981.5429-0.301-0.2837-1.14450.0614-0.27370.47020.08090.00560.33660.00460.7511-16.385-17.24115.565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 877:988 )A877 - 988
2X-RAY DIFFRACTION2( CHAIN A AND RESID 989:1112 )A989 - 1112
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1113:1171 )A1113 - 1171
4X-RAY DIFFRACTION4( CHAIN E AND RESID 528:531 )E528 - 531

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