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- PDB-4zn5: YopH W354Y Yersinia enterocolitica PTPase bond with Divanadate gl... -

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Basic information

Entry
Database: PDB / ID: 4zn5
TitleYopH W354Y Yersinia enterocolitica PTPase bond with Divanadate glycerol ester in the active site
ComponentsTyrosine-protein phosphatase YopH
KeywordsHYDROLASE/INHIBITOR / inhibitor / phosphatase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


dephosphorylation / 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 / Tyrosine-specific protein phosphatase, PTPase domain ...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
ACETATE ION / Divanadate Glycerol ester / VANADATE ION / Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsMoise, G.E. / Johnson, S.J. / Hengge, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM47297 United States
CitationJournal: Biochemistry / Year: 2015
Title: Conservative Tryptophan Mutants of the Protein Tyrosine Phosphatase YopH Exhibit Impaired WPD-Loop Function and Crystallize with Divanadate Esters in Their Active Sites.
Authors: Moise, G. / Gallup, N.M. / Alexandrova, A.N. / Hengge, A.C. / Johnson, S.J.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase YopH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0735
Polymers33,5311
Non-polymers5424
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.359, 58.003, 90.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tyrosine-protein phosphatase YopH / Virulence protein


Mass: 33530.848 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 164-468) / Mutation: C235R, W354H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yopH, yop51 / Production host: Escherichia coli (E. coli) / References: UniProt: P15273, protein-tyrosine-phosphatase

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Non-polymers , 5 types, 457 molecules

#2: Chemical ChemComp-DVG / Divanadate Glycerol ester


Mass: 275.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10O8V2
#3: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES / PH range: 7.5 / Temp details: room temp

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Data collection

DiffractionMean temperature: 195 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. all: 106319 / Num. obs: 106319 / % possible obs: 96.2 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.04 / Rsym value: 0.02 / Net I/σ(I): 46.7
Reflection shellResolution: 1.12→1.16 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 6.1 / % possible all: 78

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.15data extraction
AUTOMARdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F99

3f99


Resolution: 1.12→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.145 5292 10 %random selection
Rwork0.129 ---
obs0.1292 106319 96.2 %-
Displacement parametersBiso max: 52.9 Å2 / Biso mean: 15.6163 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: LAST / Resolution: 1.12→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 28 453 2645
LS refinement shellResolution: 1.129→1.134 Å
RfactorNum. reflection% reflection
Rfree0.1687 139 -
Rwork0.1442 2578 -
obs--75 %

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