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- PDB-2i42: Crystal structure of Yersinia protein tyrosine phosphatase comple... -

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Basic information

Entry
Database: PDB / ID: 2i42
TitleCrystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue
ComponentsTyrosine-protein phosphatase
KeywordsHYDROLASE / Yersinia PTPase / vanadate / transition state analogue
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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsVijayalakshmi, J. / Saper, M.A.
Citation
Journal: To be Published
Title: Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue
Authors: Vijayalakshmi, J. / Saper, M.A.
#1: Journal: PROC.NATL.ACAD.SCI.USA / Year: 1995
Title: Visualization of intermediate and transition-state structures in protein tyrosine phosphatase catalysis.
Authors: Denu, J.M. / Lohse, D.L. / Vijayalakshmi, J. / Saper, M.A. / Dixon, J.E.
#2: 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.
#3: 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.
History
DepositionAug 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2013Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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
Remark 600HETEROGEN VANADATE IS IN A TRIGONAL BIPYRAMIDAL GEOMETRY AND THE VANADIUM ATOM IS COVALENTLY BONDED ...HETEROGEN VANADATE IS IN A TRIGONAL BIPYRAMIDAL GEOMETRY AND THE VANADIUM ATOM IS COVALENTLY BONDED TO SG ATOM OF CYS 403 WITH A BONDING DISTANCE OF 2.52 A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6692
Polymers33,5541
Non-polymers1151
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.390, 49.660, 100.390
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 Tyrosine-protein phosphatase / Virulence protein


Mass: 33553.883 Da / Num. of mol.: 1 / Fragment: Tyrosine-protein phosphatase / Mutation: C235R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: W22703 / Gene: yopH, yop51 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15273, protein-tyrosine-phosphatase
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.26 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 400 mM NaCl, 14% PEG 4K, 5% 2-proponol .15% BME, 100mM Tris HCl pH 8.5, 1mM vanadate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 13593 / Num. obs: 13593 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 4.02 % / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.25 / Num. unique all: 1336 / % possible all: 74.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
MADNESSdata collection
XSCALEdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entries 1YTW and 1YTS

1ytw

1yts


Resolution: 2.2→7 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Residues Met163-Val186 were not included in the refinement due to missing electron densities.
RfactorNum. reflection
Rwork0.17 -
obs0.17 11701
Displacement parametersBiso mean: 17.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 5 183 2354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d2.1
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rwork0.231 --
obs-1108 61.6 %

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