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- PDB-4ri4: Crystal structure of PTPN3 (PTPH1) Y676I mutant in complex with v... -

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Basic information

Entry
Database: PDB / ID: 4ri4
TitleCrystal structure of PTPN3 (PTPH1) Y676I mutant in complex with vanadate
ComponentsTyrosine-protein phosphatase non-receptor type 3
KeywordsHYDROLASE / Alpha Beta
Function / homology
Function and homology information


regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transport / negative regulation of mitotic cell cycle / negative regulation of epidermal growth factor receptor signaling pathway / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transport / negative regulation of mitotic cell cycle / negative regulation of epidermal growth factor receptor signaling pathway / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / EGFR downregulation / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / MAPK cascade / ATPase binding / cytoskeleton / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, 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-3, -4 / PTPN3/4, 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 / Protein tyrosine phosphatase superfamily / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / Tyrosine-protein phosphatase non-receptor type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.596 Å
AuthorsChen, K.-E. / Meng, T.C. / Wang, A.H.-J.
CitationJournal: Structure / Year: 2015
Title: Substrate specificity and plasticity of FERM-containing protein tyrosine phosphatases.
Authors: Chen, K.E. / Li, M.Y. / Chou, C.C. / Ho, M.R. / Chen, G.C. / Meng, T.C. / Wang, A.H.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Advisory / Data collection / Database references
Category: citation / diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 3
B: Tyrosine-protein phosphatase non-receptor type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0254
Polymers69,7952
Non-polymers2302
Water9,638535
1
A: Tyrosine-protein phosphatase non-receptor type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0132
Polymers34,8981
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0132
Polymers34,8981
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.878, 99.406, 134.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 3


Mass: 34897.719 Da / Num. of mol.: 2 / Fragment: Catalytic domain (UNP RESIDUES 628-909) / Mutation: Y676I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPH1, PTPN3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P26045, protein-tyrosine-phosphatase
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Tris-HCl, 25% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 15, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.596→30 Å / Num. all: 83163 / Num. obs: 83163 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.5 / Num. unique all: 8085 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-IceGUIdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RH5

4rh5


Resolution: 1.596→23.996 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 18.51 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 4141 4.98 %RANDOM
Rwork0.1631 ---
all0.1643 83163 --
obs0.1643 83120 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.596→23.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 10 535 5039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014724
X-RAY DIFFRACTIONf_angle_d1.2876464
X-RAY DIFFRACTIONf_dihedral_angle_d13.3521792
X-RAY DIFFRACTIONf_chiral_restr0.062745
X-RAY DIFFRACTIONf_plane_restr0.007833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5961-1.61420.31571170.223214282
1.6142-1.63320.22781440.2077258398
1.6332-1.65310.22131290.20052631100
1.6531-1.6740.25061370.192678100
1.674-1.69610.22171330.19082614100
1.6961-1.71930.23611430.18882670100
1.7193-1.74380.25311300.18592618100
1.7438-1.76990.25021430.17822657100
1.7699-1.79750.23261280.17662661100
1.7975-1.8270.20391280.17522626100
1.827-1.85850.22291540.17642688100
1.8585-1.89220.23191440.16952607100
1.8922-1.92860.18451460.17022641100
1.9286-1.9680.22831590.17322638100
1.968-2.01070.22381420.17362653100
2.0107-2.05750.20441480.16962632100
2.0575-2.10890.20121340.16582657100
2.1089-2.16590.1811590.1692640100
2.1659-2.22960.20731460.16052628100
2.2296-2.30150.19361320.1579265699
2.3015-2.38370.18381450.155262399
2.3837-2.4790.16621340.1522264799
2.479-2.59170.17581370.1527263099
2.5917-2.72820.19061260.1579266299
2.7282-2.89890.19231160.173267199
2.8989-3.12220.18011330.1719267799
3.1222-3.43560.19111350.1664269399
3.4356-3.93090.17321370.1574262897
3.9309-4.94540.14521390.1352266497
4.9454-23.99880.17261430.1617276497

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