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- PDB-2y2f: Crystal structure of Yersinia pestis YopH in complex with an amin... -

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Basic information

Entry
Database: PDB / ID: 2y2f
TitleCrystal structure of Yersinia pestis YopH in complex with an aminooxy- containing platform compound for inhibitor design
ComponentsPROTEIN-TYROSINE PHOSPHATASE YOPH
KeywordsHYDROLASE / PROTEIN TYROSINE PHOSPHATASE
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
Chem-YI1 / protein-tyrosine-phosphatase / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLountos, G.T. / Bahta, M. / Dyas, B. / Ulrich, R.G. / Waugh, D.S. / Burke, T.R.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Utilization of Nitrophenylphosphates and Oxime-Based Ligation for the Development of Nanomolar Affinity Inhibitors of the Yersinia Pestis Outer Protein H (Yoph) Phosphatase.
Authors: Bahta, M. / Lountos, G.T. / Dyas, B. / Kim, S. / Ulrich, R.G. / Waugh, D.S. / Burke, T.R.
History
DepositionDec 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Version format compliance
Revision 1.2Dec 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: PROTEIN-TYROSINE PHOSPHATASE YOPH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8842
Polymers33,5541
Non-polymers3301
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.243, 55.480, 100.081
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 PROTEIN-TYROSINE PHOSPHATASE YOPH / UNCHARACTERIZED PROTEIN YOPH / UNCHARACTERIZED PROTEIN YPCD1.67C


Mass: 33553.883 Da / Num. of mol.: 1 / Fragment: PTPASE 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) / References: UniProt: Q7ARH8, UniProt: O68720*PLUS
#2: Chemical ChemComp-YI1 / [4-[3-(DIFLUORO-PHOSPHONO-METHYL)PHENYL]PHENYL]METHOXYAZANIUM


Mass: 330.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15F2NO4P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.04 Å3/Da / Density % sol: 39.57 % / Description: NONE
Crystal growpH: 7.5
Details: MOLECULAR DIMENSIONS MORPHEUS SCREEN CONDITION D8 (0.1M BUFFER SYSTEM 2, PH 7.5, 0.12M ALCOHOLS, 12.5% V/V MPD, 12.5% W/V PEG 1000, 12.5% W/V PEG 3350).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARESEARCH MX-300 / Detector: CCD / Date: Aug 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 25241 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.9
Reflection shellResolution: 1.78→1.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.3 / % possible all: 74.8

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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: 1.78→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.431 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21007 1268 5 %RANDOM
Rwork0.16457 ---
obs0.16685 23875 92.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.168 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.9 Å20 Å2
3---1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 22 274 2461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222300
X-RAY DIFFRACTIONr_bond_other_d0.0020.021587
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9743129
X-RAY DIFFRACTIONr_angle_other_deg0.90433868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6523.585106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8551526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02461
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_it0.8131.51449
X-RAY DIFFRACTIONr_mcbond_other0.2361.5587
X-RAY DIFFRACTIONr_mcangle_it1.5422351
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5553851
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0654.5768
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: 1.775→1.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 66 -
Rwork0.282 1364 -
obs--72 %

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