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- PDB-1qz0: Crystal Structure of the Yersinia Pestis Phosphatase YopH in Comp... -

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Basic information

Entry
Database: PDB / ID: 1qz0
TitleCrystal Structure of the Yersinia Pestis Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide
Components
  • ASP-ALA-ASP-GLU-FTY-LEU-NH2
  • Protein-tyrosine phosphatase yopH
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PHOSPHATASE / PTPASE / YOPH / DEPHOSPHORYLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


symbiont-mediated suppression of host reactive oxygen species generation / symbiont-mediated disruption of host focal adhesion / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ac-DADE-F(2)Pmp-L-NH(2) / : / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPhan, J. / Lee, K. / Cherry, S. / Tropea, J.E. / Burke Jr, T.R. / Waugh, D.S.
CitationJournal: Biochemistry / Year: 2003
Title: High-Resolution Structure of the Yersinia pestis Protein Tyrosine Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide
Authors: Phan, J. / Lee, K. / Cherry, S. / Tropea, J.E. / Burke Jr, T.R. / Waugh, D.S.
History
DepositionSep 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 30, 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: ASP-ALA-ASP-GLU-FTY-LEU-NH2
D: ASP-ALA-ASP-GLU-FTY-LEU-NH2
E: ASP-ALA-ASP-GLU-FTY-LEU-NH2
F: ASP-ALA-ASP-GLU-FTY-LEU-NH2


Theoretical massNumber of molelcules
Total (without water)70,4556
Polymers70,4556
Non-polymers00
Water10,863603
1
A: Protein-tyrosine phosphatase yopH
C: ASP-ALA-ASP-GLU-FTY-LEU-NH2
D: ASP-ALA-ASP-GLU-FTY-LEU-NH2


Theoretical massNumber of molelcules
Total (without water)35,2273
Polymers35,2273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-11 kcal/mol
Surface area12340 Å2
MethodPISA
2
B: Protein-tyrosine phosphatase yopH
E: ASP-ALA-ASP-GLU-FTY-LEU-NH2
F: ASP-ALA-ASP-GLU-FTY-LEU-NH2


Theoretical massNumber of molelcules
Total (without water)35,2273
Polymers35,2273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-12 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.292, 53.450, 69.066
Angle α, β, γ (deg.)109.61, 104.75, 89.98
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 33553.883 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, Residues 164-468 / Mutation: C235R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Plasmid: pZZ1089 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 16082755, UniProt: O68720*PLUS, protein-tyrosine-phosphatase
#2: Protein/peptide
ASP-ALA-ASP-GLU-FTY-LEU-NH2


Type: Peptide-like / Class: Inhibitor / Mass: 836.710 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: Ac-DADE-F(2)Pmp-L-NH(2)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 100 mM HEPES, 100 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110.3 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.5
320 %(w/v)PEG40001reservoir
410 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97148 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2002 / Details: Mirrors
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97148 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 87736 / Num. obs: 87736 / % possible obs: 68 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 1.9 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.038 / Net I/σ(I): 17
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6162 / % possible all: 68
Reflection
*PLUS
% possible obs: 89.3 % / Rmerge(I) obs: 0.038

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YPT

1ypt


Resolution: 1.5→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.8 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 6702 -Random
Rwork0.188 ---
all-87736 --
obs-66557 76 %-
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 0 603 5137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 1.5→1.51 Å /
RfactorNum. reflection
Rfree0.237 -
Rwork0.211 -
obs-321

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