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- PDB-1pa9: Yersinia Protein-Tyrosine Phosphatase complexed with pNCS (Yop51,... -

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Basic information

Entry
Database: PDB / ID: 1pa9
TitleYersinia Protein-Tyrosine Phosphatase complexed with pNCS (Yop51,Pasteurella X,Ptpase,Yop51delta162) (Catalytic Domain, Residues 163-468) Mutant With Cys 235 Replaced By Arg (C235r)
ComponentsProtein-tyrosine phosphatase yopH
KeywordsHYDROLASE / VIRULENCE
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
N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM / Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSun, J.P. / Wu, L. / Fedorov, A.A. / Almo, S.C. / Zhang, Z.Y.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Crystal structure of the Yersinia protein-tyrosine phosphatase YopH complexed with a specific small molecule inhibitor
Authors: Sun, J.P. / Wu, L. / Fedorov, A.A. / Almo, S.C. / Zhang, Z.Y.
History
DepositionMay 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 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 yopH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4882
Polymers31,2521
Non-polymers2351
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.360, 55.900, 97.840
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 Protein-tyrosine phosphatase yopH / Virulence protein


Mass: 31252.383 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: C73R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: YOPH OR 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-CSN / N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM


Mass: 235.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG1500, imdazole, pNCS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
210 mMimidazole1droppH7.2
30.2 mMEDTA1drop
40.1 %beta-mercaptoethanol1drop
55 mMpNCS inhibitor1drop
620 mMimidazole1reservoirpH7.2
720 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Mar 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 17749 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.314 / % possible all: 91.1
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 91.1 %

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Processing

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

1ytw


Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 688 -RANDOM
Rwork0.226 ---
obs0.227 17749 92.5 %-
all-19188 --
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 15 217 2381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.29
X-RAY DIFFRACTIONc_bond_d0.005
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.29

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