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Basic information

Entry
Database: PDB / ID: 1ytn
TitleHYDROLASE
ComponentsYERSINIA PROTEIN TYROSINE PHOSPHATASE
KeywordsHYDROLASE / PROTEIN TYROSINE PHOSPHATASE
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.4 Å
AuthorsYuvaniyama, C. / Fauman, E.B. / Saper, M.A.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: The X-ray crystal structures of Yersinia tyrosine phosphatase with bound tungstate and nitrate. Mechanistic implications.
Authors: Fauman, E.B. / Yuvaniyama, C. / Schubert, H.L. / Stuckey, J.A. / Saper, M.A.
#1: 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.
#2: Journal: Nature / Year: 1994
Title: Crystal Structure of Yersinia Protein Tyrosine Phosphatase at 2.5 A 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. / Hume, D.M. / Saper, M.A. / Dixon, J.E.
History
DepositionMay 1, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)33,6162
Polymers33,5541
Non-polymers621
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.700, 49.700, 99.500
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 / YOP51 / YOP2B / PASTEURELLA X / PTP-ASE / YOP51DELTA162


Mass: 33553.883 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 163 - 468
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH NITRATE / Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: W22703 / Cell line: BL21 / Gene: YOP51 / Plasmid: PT7-7 / Species (production host): Escherichia coli / Gene (production host): YOP51 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15273, protein-tyrosine-phosphatase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.09 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS BY THE HANGING DROP VAPOR DIFFUSION METHOD. DROP WAS COMPOSED OF EQUAL VOLUMES OF PROTEIN (23 MG/ML) ...Details: THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 23 DEGREES CELSIUS BY THE HANGING DROP VAPOR DIFFUSION METHOD. DROP WAS COMPOSED OF EQUAL VOLUMES OF PROTEIN (23 MG/ML) AND RESERVOIR SOLUTION. RESERVOIR SOLUTION WAS 27% POLYETHYLENE GLYCOL (MW 1500), 10% 2-METHYL-2,4-PENTANEDIOL, 220 MM SODIUM NITRATE, 0.1% BETA-MERCAPTOETHANOL, AND 10 MM IMIDAZOLE, PH 7.2., vapor diffusion - hanging drop, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
123 mg/mlPTPase1drop
327 %(w/v)PEG15001reservoirprecipitant
410 %MPD1reservoirprecipitant
50.1 %beta-mercaptoethanol1reservoirprecipitant
6220 mMsodium nitrate1reservoirprecipitant
710 mMimidazole1reservoirprecipitant
2precipitant1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 17, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9205 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.49 % / Rmerge(I) obs: 0.115
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 9999 Å
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 66 % / Rmerge(I) obs: 0.226

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
MADNESdata reduction
PROCORdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1YTW

1ytw


Resolution: 2.4→7 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.181 --
obs0.181 9205 98 %
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1-5.098 Å20 Å20 Å2
2--9.347 Å20 Å2
3----14.445 Å2
Refinement stepCycle: LAST / Resolution: 2.4→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 4 105 2282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
LS refinement shellResolution: 2.4→2.5 Å /
Rfactor% reflection
Rwork0.268 -
obs-66 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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