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- PDB-1x24: Prl-1 (ptp4a) -

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Basic information

Entry
Database: PDB / ID: 1x24
TitlePrl-1 (ptp4a)
Componentsprotein tyrosine phosphatase 4a1
KeywordsHYDROLASE / tyrosine phosphatase / prl-1 / dual specific phosphatase
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / spindle / early endosome / positive regulation of cell migration / cell cycle / endoplasmic reticulum ...protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / spindle / early endosome / positive regulation of cell migration / cell cycle / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein tyrosine phosphatase type IVA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZhang, Z.Y. / Sun, J.P. / Liu, S. / Wang, W.Q. / Yang, H.
CitationJournal: Biochemistry / Year: 2005
Title: Structure and Biochemical Properties of PRL-1, a Phosphatase Implicated in Cell Growth, Differentiation, and Tumor Invasion(,)
Authors: Sun, J.P. / Wang, W.Q. / Yang, H. / Liu, S. / Liang, F. / Fedorov, A.A. / Almo, S.C. / Zhang, Z.Y.
History
DepositionApr 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein tyrosine phosphatase 4a1
B: protein tyrosine phosphatase 4a1


Theoretical massNumber of molelcules
Total (without water)41,0862
Polymers41,0862
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.891, 146.891, 146.891
Angle α, β, γ (deg.)90, 90, 90
Int Tables number199
Space group name H-MI213

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Components

#1: Protein protein tyrosine phosphatase 4a1 / prl-1 / ptp4a1


Mass: 20542.873 Da / Num. of mol.: 2 / Fragment: residues 1-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21 / References: UniProt: Q78EG7, protein-tyrosine-phosphatase

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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: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.8
Details: 100mM AcNa, 2.0M Ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A
DetectorDate: Feb 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 8744 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.3 Å / % possible all: 97.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.285 907 RANDOM
Rwork0.241 --
obs-8744 -
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 0 2452

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