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- PDB-1wch: Crystal structure of PTPL1 human tyrosine phosphatase mutated in ... -

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Basic information

Entry
Database: PDB / ID: 1wch
TitleCrystal structure of PTPL1 human tyrosine phosphatase mutated in colorectal cancer - evidence for a second phosphotyrosine substrate recognition pocket
ComponentsPROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 13
KeywordsHYDROLASE / TYROSINE PHOSPHATASE / PHOSPHATE ION / COLORECTAL CANCER ALTERNATIVE SPLICING / COILED COIL / CYTOSKELETON / POLYMORPHISM / STRUCTURAL PROTEIN
Function / homology
Function and homology information


negative regulation of excitatory synapse assembly / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation ...negative regulation of excitatory synapse assembly / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of protein phosphorylation / fibrillar center / lamellipodium / cell body / cytoskeleton / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / 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 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 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
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsVilla, F. / Deak, M. / Bloomberg, G.B. / Alessi, D.R. / Van Aalten, D.M.F.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Ptpl1/Fap-1 Human Tyrosine Phosphatase Mutated in Colorectal Cancer: Eveidence for a Second Phosphotyrosine Substrate Recognition Pocket
Authors: Villa, F. / Deak, M. / Bloomberg, G.B. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionNov 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3724
Polymers36,0881
Non-polymers2853
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.707, 59.193, 66.075
Angle α, β, γ (deg.)90.00, 113.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 13 / PROTEIN TYROSINE PHOSPHATASE LIKE 1 / PROTEIN TYROSINE PHOSPHATASE 1E / PTP-E1 / HPTPE1 / PTP-BAS / ...PROTEIN TYROSINE PHOSPHATASE LIKE 1 / PROTEIN TYROSINE PHOSPHATASE 1E / PTP-E1 / HPTPE1 / PTP-BAS / PROTEIN TYROSINE PHOSPHATASE PTPL1 / FAS-ASSOCIATED PROTEIN TYROSINE PHOSPHATASE 1 / FAP-1


Mass: 36087.543 Da / Num. of mol.: 1 / Fragment: RESIDUES 2163-2477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6_1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q12923, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: REGULATES NEGATIVELY FAS-INDUCED APOPTOSIS AND NGFR- MEDIATED PRO-APOPTOTIC SIGNALING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.8 %
Crystal growMethod: vapor diffusion

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 23, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 29500 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.6 / % possible all: 82.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAX

1aax


Resolution: 1.85→19.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2129463.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.204 612 2.1 %RANDOM
Rwork0.177 ---
obs0.177 29499 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2413 Å2 / ksol: 0.38548 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1--5.64 Å20 Å2-1.21 Å2
2--9.93 Å20 Å2
3----4.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 15 280 2767
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 73 1.7 %
Rwork0.247 4155 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2WATER.TOP

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