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- PDB-1zcl: prl-1 c104s mutant in complex with sulfate -

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Basic information

Entry
Database: PDB / ID: 1zcl
Titleprl-1 c104s mutant in complex with sulfate
Componentsprotein tyrosine phosphatase 4a1
KeywordsHYDROLASE / prl-1 ptp4a dual specific phosphatase
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / spindle / cytoplasmic side of plasma membrane / early endosome / positive regulation of cell migration / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
: / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases domain profile. ...: / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / 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: 2.9 Å
AuthorsSun, J.P. / Wang, W.Q. / Yang, H. / Liu, S. / Liang, F. / Fedorov, A.A. / Almo, S.C. / Zhang, Z.Y.
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 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,2464
Polymers41,0542
Non-polymers1922
Water00
1
A: protein tyrosine phosphatase 4a1
hetero molecules

A: protein tyrosine phosphatase 4a1
hetero molecules

A: protein tyrosine phosphatase 4a1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8696
Polymers61,5803
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
2
B: protein tyrosine phosphatase 4a1
hetero molecules

B: protein tyrosine phosphatase 4a1
hetero molecules

B: protein tyrosine phosphatase 4a1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8696
Polymers61,5803
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Unit cell
Length a, b, c (Å)146.681, 146.681, 146.681
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


Mass: 20526.807 Da / Num. of mol.: 2 / Mutation: c104s
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q78EG7, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Ammonium Sulfate, Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2
DetectorType: RIGAKU AFC-5 / Detector: CCD / Date: Nov 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 10372 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3 Å / % possible all: 99.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RXD

1rxd


Resolution: 2.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.296 476 RANDOM
Rwork0.261 --
obs-9778 -
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 10 0 2461

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