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- PDB-4ri5: Crystal structure of PTPN3 (PTPH1) D811E mutant in complex with m... -

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Basic information

Entry
Database: PDB / ID: 4ri5
TitleCrystal structure of PTPN3 (PTPH1) D811E mutant in complex with metavanadate
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 transporter activity / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase ...regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transporter activity / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / liver regeneration / EGFR downregulation / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / MAPK cascade / ATPase binding / cytoskeleton / plasma membrane / cytosol / cytoplasm
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. / Protein-Tyrosine Phosphatase; Chain A / 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 / 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
oxido(dioxo)vanadium / Tyrosine-protein phosphatase non-receptor type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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)70,3066
Polymers69,9242
Non-polymers3824
Water13,637757
1
A: Tyrosine-protein phosphatase non-receptor type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1533
Polymers34,9621
Non-polymers1912
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)35,1533
Polymers34,9621
Non-polymers1912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.162, 96.071, 141.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1213-

HOH

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Components

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


Mass: 34961.762 Da / Num. of mol.: 2 / Fragment: Catalytic domain (UNP RESIDUES 628-909) / Mutation: D811E
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 21% PEG 800, 5% glycerol, pH 8.5, 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: Apr 16, 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: 1.26→30 Å / Num. all: 170606 / Num. obs: 170606 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 37.1
Reflection shellResolution: 1.26→1.31 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.2 / Num. unique all: 15626 / % possible all: 90.3

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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: 1.26→25.535 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 19.12 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 7401 5.06 %RANDOM
Rwork0.1591 ---
all0.1599 170606 --
obs0.1599 146326 84.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.26→25.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 20 757 5309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114876
X-RAY DIFFRACTIONf_angle_d1.3926695
X-RAY DIFFRACTIONf_dihedral_angle_d13.9421877
X-RAY DIFFRACTIONf_chiral_restr0.077766
X-RAY DIFFRACTIONf_plane_restr0.006868
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 (%)
1.2599-1.27420.1754720.1764126923
1.2742-1.28920.1933790.1773153328
1.2892-1.30490.18211110.1748184134
1.3049-1.32140.20731230.1856233543
1.3214-1.33880.20421450.1918291553
1.3388-1.35720.18781810.1987344662
1.3572-1.37660.20742030.1904376369
1.3766-1.39710.22612280.1875407375
1.3971-1.41890.20252210.1909446181
1.4189-1.44220.19712580.1817481288
1.4422-1.46710.21332980.1877523896
1.4671-1.49370.18273070.1795537699
1.4937-1.52250.18592970.17565477100
1.5225-1.55350.19172820.17055484100
1.5535-1.58730.19382800.16785488100
1.5873-1.62420.1672670.16775501100
1.6242-1.66480.19572930.16845495100
1.6648-1.70980.17862960.16465482100
1.7098-1.76010.18292870.16565511100
1.7601-1.81690.16742870.1675469100
1.8169-1.88190.18472600.16325562100
1.8819-1.95720.16862800.1612545799
1.9572-2.04620.16693040.1591547799
2.0462-2.1540.15913080.1511544299
2.154-2.28890.15513030.149547599
2.2889-2.46550.16642840.1457551799
2.4655-2.71340.17692940.1513544998
2.7134-3.10540.1712680.159536596
3.1054-3.91020.15363150.1509522093
3.9102-25.54040.18812700.1577499286

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