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- PDB-2b49: Crystal Structure of the Catalytic Domain of Protein Tyrosine Pho... -

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Basic information

Entry
Database: PDB / ID: 2b49
TitleCrystal Structure of the Catalytic Domain of Protein Tyrosine Phosphatase, non-receptor Type 3
Componentsprotein tyrosine phosphatase, non-receptor type 3
KeywordsHYDROLASE / Protein Tyrosine Phosphatase / non-receptor Type / Human / Structural Genomics / Structural Genomics Consortium / SGC
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
Tyrosine-protein phosphatase non-receptor type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsUgochukwu, E. / Arrowsmith, C. / Barr, A. / Bunkoczi, G. / Das, S. / Debreczeni, J. / Edwards, A. / Eswaran, J. / Knapp, S. / Sundstrom, M. ...Ugochukwu, E. / Arrowsmith, C. / Barr, A. / Bunkoczi, G. / Das, S. / Debreczeni, J. / Edwards, A. / Eswaran, J. / Knapp, S. / Sundstrom, M. / Turnbull, A. / von Delft, F. / Weigelt, J. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome.
Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionSep 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein tyrosine phosphatase, non-receptor type 3


Theoretical massNumber of molelcules
Total (without water)32,7471
Polymers32,7471
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.675, 61.242, 75.885
Angle α, β, γ (deg.)90.00, 101.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein protein tyrosine phosphatase, non-receptor type 3


Mass: 32747.457 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P26045, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.2 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Ammonium Sulphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.54→43.39 Å / Num. obs: 41752 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.54→1.62 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8K.pdb

1l8k


Resolution: 1.54→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.933 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23014 2111 5.1 %RANDOM
Rwork0.19883 ---
all0.20048 39496 --
obs0.20048 39496 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.927 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-1.26 Å2
2---0.3 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.54→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 0 229 2297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222217
X-RAY DIFFRACTIONr_bond_other_d0.0010.021986
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.953049
X-RAY DIFFRACTIONr_angle_other_deg0.94134641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93224.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6421513
X-RAY DIFFRACTIONr_chiral_restr0.1570.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined0.2040.2419
X-RAY DIFFRACTIONr_nbd_other0.180.22007
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21082
X-RAY DIFFRACTIONr_nbtor_other0.0810.21315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4350.210
X-RAY DIFFRACTIONr_mcbond_it1.70231389
X-RAY DIFFRACTIONr_mcbond_other0.4693537
X-RAY DIFFRACTIONr_mcangle_it2.55352235
X-RAY DIFFRACTIONr_scbond_it3.8248941
X-RAY DIFFRACTIONr_scangle_it5.41611798
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 158 -
Rwork0.272 2854 -
obs--97.51 %
Refinement TLS params.Method: refined / Origin x: 14.0445 Å / Origin y: 13.8071 Å / Origin z: 21.1315 Å
111213212223313233
T-0.0387 Å2-0.0415 Å2-0.0156 Å2--0.0323 Å20.01 Å2---0.0522 Å2
L0.891 °2-0.293 °20.5358 °2-2.3989 °20.3156 °2--1.2279 °2
S-0.0522 Å °0.1367 Å °-0.0252 Å °-0.3867 Å °0.0744 Å °0.2552 Å °-0.0335 Å °0.1919 Å °-0.0223 Å °

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