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- PDB-1xxv: Yersinia YopH (residues 163-468) binds phosphonodifluoromethyl-Ph... -

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Basic information

Entry
Database: PDB / ID: 1xxv
TitleYersinia YopH (residues 163-468) binds phosphonodifluoromethyl-Phe containing hexapeptide at two sites
Components
  • Epidermal growth factor receptor derived peptide
  • Protein-tyrosine phosphatase yopH
KeywordsHYDROLASE / catalytic domain / phosphotyrosine-binding sites / substrate targeting
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
Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 8, 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: Version format compliance
Revision 1.3Sep 14, 2011Group: Non-polymer description
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...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 / struct_conn / 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_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine phosphatase yopH
B: Protein-tyrosine phosphatase yopH
C: Epidermal growth factor receptor derived peptide
D: Epidermal growth factor receptor derived peptide
E: Epidermal growth factor receptor derived peptide
F: Epidermal growth factor receptor derived peptide


Theoretical massNumber of molelcules
Total (without water)70,4916
Polymers70,4916
Non-polymers00
Water5,350297
1
A: Protein-tyrosine phosphatase yopH
C: Epidermal growth factor receptor derived peptide
D: Epidermal growth factor receptor derived peptide


Theoretical massNumber of molelcules
Total (without water)35,2453
Polymers35,2453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-9 kcal/mol
Surface area12300 Å2
MethodPISA
2
B: Protein-tyrosine phosphatase yopH
E: Epidermal growth factor receptor derived peptide
F: Epidermal growth factor receptor derived peptide


Theoretical massNumber of molelcules
Total (without water)35,2453
Polymers35,2453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-12 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.130, 47.170, 71.820
Angle α, β, γ (deg.)104.45, 115.05, 89.97
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 33519.805 Da / Num. of mol.: 2 / Fragment: Catalytic domain, residues 163-468 / Mutation: 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
Epidermal growth factor receptor derived peptide


Mass: 862.748 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: chemically synthesized by Robert Zamboni and Michael Gresser, Merck Frosst, Montreal
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 45.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mg/ml protein, 0.5 mM phosphonodifluoro-Phe-containing peptide in 1 mM imidazole. Precipitant: 22% polyethylene glycol (PEG) 4000, 8 mM MnCl2, 0.1% beta-mercaptoethanol, 100 mM Hepes, pH ...Details: 10 mg/ml protein, 0.5 mM phosphonodifluoro-Phe-containing peptide in 1 mM imidazole. Precipitant: 22% polyethylene glycol (PEG) 4000, 8 mM MnCl2, 0.1% beta-mercaptoethanol, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / 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: 2.5→50 Å / Num. all: 18319 / Num. obs: 18319 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.075

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
MERLOTphasing
CNSrefinement
SDMSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: YopH (residues 163-468) with bound VO4 (not submitted to PDB)

Resolution: 2.5→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: restrained B refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.229 892 -random
Rwork0.178 ---
all-18319 --
obs-18319 85.5 %-
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 0 297 4831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.183
X-RAY DIFFRACTIONc_scbond_it2.138
LS refinement shellResolution: 2.5→2.55 Å /
RfactorNum. reflection
Rfree0.298 38
Rwork0.204 -
obs-853

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