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- PDB-1xxp: Yersinia YopH (residues 163-468) C403S binds phosphotyrosyl pepti... -

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Basic information

Entry
Database: PDB / ID: 1xxp
TitleYersinia YopH (residues 163-468) C403S binds phosphotyrosyl peptide at two sites
Components
  • Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE
  • Protein-tyrosine phosphatase yopH
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Peptide binds at site remote from catalytic site. Important for protein localization in infected cell. / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsIvanov, M.I. / Stuckey, J.A. / Schubert, H.L. / Saper, M.A. / Bliska, J.B.
CitationJournal: Mol.Microbiol. / Year: 2005
Title: Two substrate-targeting sites in the Yersinia protein tyrosine phosphatase co-operate to promote bacterial virulence
Authors: Ivanov, M.I. / Stuckey, J.A. / Schubert, H.L. / Saper, M.A. / Bliska, J.B.
History
DepositionNov 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine phosphatase yopH
B: Protein-tyrosine phosphatase yopH
C: Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE
D: Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE
E: Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE
F: Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE


Theoretical massNumber of molelcules
Total (without water)70,3226
Polymers70,3226
Non-polymers00
Water1,49583
1
A: Protein-tyrosine phosphatase yopH
C: Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE
D: Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE


Theoretical massNumber of molelcules
Total (without water)35,1613
Polymers35,1613
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area12640 Å2
MethodPISA
2
B: Protein-tyrosine phosphatase yopH
E: Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE
F: Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE


Theoretical massNumber of molelcules
Total (without water)35,1613
Polymers35,1613
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-10 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.170, 71.090, 47.860
Angle α, β, γ (deg.)111.80, 90.00, 109.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein-tyrosine phosphatase yopH / Virulence protein


Mass: 33503.738 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, residues 163-468 / Mutation: C403S, C235R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / 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: Protein/peptide
Hexapeptide ASP-ALA-ASP-GLU-PTR-CLE


Mass: 828.739 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10-12 mg/ml protein + 1 mM phosphopeptide. Precipitant: 18-24% polyethylene glycol (PEG) 8000, 50-100 mM NaCl, 0.1% beta-mercaptoethanol, 100 mM TrisCl, pH 8.5, 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: UCSD MARK III / Detector: AREA DETECTOR / Details: monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 10470 / Num. obs: 10084 / % possible obs: 86 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.118

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
CNSrefinement
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YTS

1yts


Resolution: 3→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: restrained B refinement
RfactorNum. reflectionSelection details
Rfree0.25 534 random
Rwork0.181 --
all-10470 -
obs-10084 -
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 0 83 4580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0076
X-RAY DIFFRACTIONc_angle_deg1.177

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