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- PDB-4qun: Crystal structure of the PTPN3 (PTPH1) catalytic domain C842S mutant -

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Basic information

Entry
Database: PDB / ID: 4qun
TitleCrystal structure of the PTPN3 (PTPH1) catalytic domain C842S mutant
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 / Protein tyrosine phosphatase superfamily / FERM central domain / FERM superfamily, second domain / Protein-Tyrosine Phosphatase; Chain A / 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 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
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsChen, K.E. / Meng, T.C. / Wang, A.H.J.
CitationJournal: Sci.Signal. / Year: 2014
Title: Reciprocal allosteric regulation of p38 gamma and PTPN3 involves a PDZ domain-modulated complex formation.
Authors: Chen, K.E. / Lin, S.Y. / Wu, M.J. / Ho, M.R. / Santhanam, A. / Chou, C.C. / Meng, T.C. / Wang, A.H.J.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...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 / 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)70,1455
Polymers69,8632
Non-polymers2823
Water6,089338
1
A: Tyrosine-protein phosphatase non-receptor type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0272
Polymers34,9321
Non-polymers951
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)35,1193
Polymers34,9321
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.740, 97.000, 138.207
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 / Protein-tyrosine phosphatase H1 / PTP-H1


Mass: 34931.672 Da / Num. of mol.: 2 / Fragment: Catalytic domain (UNP RESIDUES 628-909) / Mutation: C842S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPH1, PTPN3 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P26045, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 45.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 12% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 9, 2012
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 53391 / Num. obs: 53391 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5319 / % possible all: 100

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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 2B49

2b49


Resolution: 1.86→45.764 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 2715 5.09 %RANDOM
Rwork0.1771 ---
all0.1785 53391 --
obs0.1785 53350 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→45.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 16 338 4872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014739
X-RAY DIFFRACTIONf_angle_d1.266468
X-RAY DIFFRACTIONf_dihedral_angle_d14.2731800
X-RAY DIFFRACTIONf_chiral_restr0.057730
X-RAY DIFFRACTIONf_plane_restr0.005837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8597-1.89350.28111460.2363259798
1.8935-1.930.26411490.22452625100
1.93-1.96930.25071460.21182643100
1.9693-2.01220.23851530.20872633100
2.0122-2.0590.24671330.18862715100
2.059-2.11050.20831340.18112645100
2.1105-2.16750.23531490.18062638100
2.1675-2.23130.21681490.17572643100
2.2313-2.30330.20641240.17342698100
2.3033-2.38560.21321350.17792668100
2.3856-2.48120.22171590.18242663100
2.4812-2.59410.20521250.18132687100
2.5941-2.73080.23691400.18362692100
2.7308-2.90190.21661550.19572653100
2.9019-3.12590.22691480.20382696100
3.1259-3.44040.2041220.1872269099
3.4404-3.9380.19251500.1671264697
3.938-4.96050.17121550.1456262796
4.9605-45.77780.18321430.1633277697

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