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- PDB-1yts: A LIGAND-INDUCED CONFORMATIONAL CHANGE IN THE YERSINIA PROTEIN TY... -

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Basic information

Entry
Database: PDB / ID: 1yts
TitleA LIGAND-INDUCED CONFORMATIONAL CHANGE IN THE YERSINIA PROTEIN TYROSINE PHOSPHATASE
ComponentsYERSINIA PROTEIN TYROSINE PHOSPHATASE
KeywordsHYDROLASE / PROTEIN TYROSINE PHOSPHATASE
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region
Similarity search - Function
Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Protein tyrosine phosphatase superfamily / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSchubert, H.L. / Stuckey, J.A. / Fauman, E.B. / Dixon, J.E. / Saper, M.A.
Citation
Journal: Protein Sci. / Year: 1995
Title: A ligand-induced conformational change in the Yersinia protein tyrosine phosphatase.
Authors: Schubert, H.L. / Fauman, E.B. / Stuckey, J.A. / Dixon, J.E. / Saper, M.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Dissecting the Catalytic Mechanism of Protein-Tyrosine Phosphatases
Authors: Zhang, Z.-Y. / Wang, Y. / Dixon, J.E.
#2: Journal: Nature / Year: 1994
Title: Crystal Structure of Yersinia Protein Tyrosine Phosphatase at 2.5 Angstroms and the Complex with Tungstate
Authors: Stuckey, J.A. / Schubert, H.L. / Fauman, E.B. / Zhang, Z.-Y. / Dixon, J.E. / Saper, M.A.
#3: Journal: J.Biol.Chem. / Year: 1992
Title: Expression, Purification, and Physicochemical Characterization of a Recombinant Yersinia Protein Tyrosine Phosphatase
Authors: Zhang, Z.-Y. / Clemens, J.C. / Schubert, H.L. / Stuckey, J.A. / Fischer, M.W.F. / Hume, D.M. / Saper, M.A. / Dixon, J.E.
History
DepositionApr 7, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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: YERSINIA PROTEIN TYROSINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8243
Polymers30,6321
Non-polymers1922
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.400, 49.800, 100.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein YERSINIA PROTEIN TYROSINE PHOSPHATASE


Mass: 30631.664 Da / Num. of mol.: 1
Mutation: CYS 235 REPLACED BY ARG, CYS 403 REPLACED BY SER, C235R, C403S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: W22703 / Gene: YOP51 / Plasmid: PT7-7 / Gene (production host): YOP51 / Production host: Escherichia coli (E. coli) / References: UniProt: P15273, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsYERSINIA PROTEIN TYROSINE PHOSPHATASE. ONLY THE CATALYTIC DOMAIN (RESIDUES 163 - 468) WAS ...YERSINIA PROTEIN TYROSINE PHOSPHATASE. ONLY THE CATALYTIC DOMAIN (RESIDUES 163 - 468) WAS CRYSTALLIZED. THE 235 CYS TO ARG MUTATION WAS UNINTENTIONAL AND MOST LIKELY THE RESULT OF USING PCR TO CONSTRUCT THE PLASMID. THE 403 CYS TO SER MUTATION ELIMINATES ALL PTPASE CATALYTIC ACTIVITY.

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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: 46.54 %
Crystal growTemperature: 296 K / pH: 8.5
Details: MOLECULE: YERSINIA PROTEIN TYROSINE PHOSPHATASE CYS(403)SER COMPLEXED WITH SULFATE. THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS, IN A SOLUTION ...Details: MOLECULE: YERSINIA PROTEIN TYROSINE PHOSPHATASE CYS(403)SER COMPLEXED WITH SULFATE. THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS, IN A SOLUTION OF 18 - 24% POLYETHYLENE GLYCOL (MW 4000), 5% 2-METHYL-2,4-PENTANEDIOL, 0.1% BETA-MERCAPTOETHANOL, 200MM LI2SO4, 0.1M TRIS-HCL, pH 8.5, temperature 296K
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
pH: 5.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-12 mg/mlprotein1drop
230 mM1dropNaCl
35 mMNa acetate1drop
418-22 %(w/v)PEG40001dropprecipitant
5200 mM1dropLi2SO4precipitant
65 %2-propanol1dropprecipitant
70.1 %2-mercaptoethanol1dropprecipitant
8100 mMTris-HCl1dropprecipitant
9precipitant1reservoir1 ml

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorDate: Jul 30, 1992
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9156 / % possible obs: 92 % / Redundancy: 2.49 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.082

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing
RefinementResolution: 2.5→10 Å /
RfactorNum. reflection
Rwork0.174 -
obs0.174 9156
Displacement parametersBiso mean: 18.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 10 60 2207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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