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- PDB-2ydu: Crystal structure of YopH in complex with 3-(1,1-dioxido-3- oxois... -

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Basic information

Entry
Database: PDB / ID: 2ydu
TitleCrystal structure of YopH in complex with 3-(1,1-dioxido-3- oxoisothiazolidin-5-yl)benzaldeyde
ComponentsOUTER PROTEIN H PHOSPHATASE
KeywordsHYDROLASE / ANTIPLAGUE DRUG DESIGN
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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-79W / protein-tyrosine-phosphatase / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsLountos, G.T. / Kim, S.E. / Bahta, M. / Ulrich, R.G. / Waugh, D.S. / Burke, T.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Isothiazolidinone (Izd) as a Phosphoryl Mimetic in Inhibitors of the Yersinia Pestis Protein Tyrosine Phosphatase Yoph.
Authors: Kim, S.E. / Bahta, M. / Lountos, G.T. / Ulrich, R.G. / Burke, T.R. / Waugh, D.S.
History
DepositionMar 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER PROTEIN H PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7922
Polymers33,5541
Non-polymers2381
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.307, 55.912, 99.055
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 OUTER PROTEIN H PHOSPHATASE / TYPE III SECRETION INJECTED VIRULENCE PROTEIN / YPCD1.67C / YOPH


Mass: 33553.883 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 164-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PZZ1089 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q7ARH8, UniProt: O68720*PLUS
#2: Chemical ChemComp-79W / 3-[(2S)-1,1-DIOXIDO-4-OXOTETRAHYDROTHIOPHEN-2-YL]BENZALDEHYDE


Mass: 238.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.03 Å3/Da / Density % sol: 39.5 % / Description: NONE
Crystal growpH: 7.5
Details: MORPHEUS E8 (0.1M BUFFER SYSTEM 2 PH 7.5, 0.12 M ETHYLENE GLYCOLS, 12.5% V/V MPD, 12.5% W/V PEG 3350, , 12.5% W/V PEG 1000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: MARRESEARCH / Date: Jun 18, 2010 / Details: VARIMAX HR-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 25845 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 35.5
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.6 / % possible all: 63.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZ0

1qz0


Resolution: 1.79→49.51 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.816 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21323 1302 5 %RANDOM
Rwork0.17589 ---
obs0.17778 24486 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.758 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.79→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 16 276 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222237
X-RAY DIFFRACTIONr_bond_other_d0.0020.021532
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9723036
X-RAY DIFFRACTIONr_angle_other_deg0.9163.0013724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15623.922102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2041523
X-RAY DIFFRACTIONr_chiral_restr0.1020.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8721.51420
X-RAY DIFFRACTIONr_mcbond_other0.221.5577
X-RAY DIFFRACTIONr_mcangle_it1.65622296
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7593817
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3994.5734
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.786→1.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 63 -
Rwork0.365 1236 -
obs--66.86 %

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