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- PDB-5ncr: OH1 from the Orf virus: a tyrosine phosphatase that displays dist... -

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Basic information

Entry
Database: PDB / ID: 5ncr
TitleOH1 from the Orf virus: a tyrosine phosphatase that displays distinct structural features and triple substrate specificity
Componentstyrosine phosphatase
KeywordsHYDROLASE / Tyrosine-phosphatase / homodimer / disulfide bridge / phosphate binding site
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein tyrosine phosphatase activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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
PHOSPHATE ION / Putative dual specificity protein phosphatase H1
Similarity search - Component
Biological speciesOrf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsSegovia, D. / Haouz, A. / Berois, M. / Villarino, A. / Andre-Leroux, G.
Funding supportUruguay, France, 5items
OrganizationGrant numberCountry
CSICUruguay
ECOS-SudUruguay
ECOS-Sud France
universidad de la RepublicaUruguay
Institut National de la Recherche Agronomique France
CitationJournal: J. Mol. Biol. / Year: 2017
Title: OH1 from Orf Virus: A New Tyrosine Phosphatase that Displays Distinct Structural Features and Triple Substrate Specificity.
Authors: Segovia, D. / Haouz, A. / Porley, D. / Olivero, N. / Martinez, M. / Mariadassou, M. / Berois, M. / Andre-Leroux, G. / Villarino, A.
History
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tyrosine phosphatase
B: tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7035
Polymers40,4172
Non-polymers2863
Water2,018112
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-44 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.558, 63.554, 55.391
Angle α, β, γ (deg.)90.000, 97.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tyrosine phosphatase / Tyrosine phosphatase / virus assembly


Mass: 20208.447 Da / Num. of mol.: 2 / Mutation: C112S
Source method: isolated from a genetically manipulated source
Details: scab from Ovis aries (sheep) / Source: (gene. exp.) Orf virus / Plasmid: pET28a(+)
Details (production host): N-terminal 6xHis-tag, and an added TEV site
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6TW43
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 30% PEG MME 2K, Na-Acetate pH 4.6, 0.2M NH42SO4

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.89 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 1.88→41.58 Å / Num. obs: 26622 / % possible obs: 95 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.56 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.094 / Rrim(I) all: 0.17 / Net I/σ(I): 4.4 / Num. measured all: 84484 / Scaling rejects: 23
Reflection shellResolution: 1.88→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.141 / CC1/2: 0.174 / Rpim(I) all: 1.538 / Rrim(I) all: 2.627 / % possible all: 95

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CM3

3cm3


Resolution: 1.89→17.73 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1324 5.01 %RANDOM
Rwork0.187 ---
obs0.189 26404 96.3 %-
Displacement parametersBiso max: 111.49 Å2 / Biso mean: 36.71 Å2 / Biso min: 14 Å2
Baniso -1Baniso -2Baniso -3
1-1.5928 Å20 Å20.9419 Å2
2---0.8917 Å20 Å2
3----0.7011 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.89→17.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 15 112 2806
Biso mean--36.29 38.05 -
Num. residues----347
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d948SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes417HARMONIC5
X-RAY DIFFRACTIONt_it2768HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion363SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3368SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2768HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3761HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion16.17
LS refinement shellResolution: 1.89→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2262 131 5.01 %
Rwork0.2241 2486 -
all0.2242 2617 -
obs--84.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8964-0.83150.74071.909-0.52162.27370.00630.1640.0591-0.0157-0.029-0.16120.0291-0.02110.0227-0.0571-0.018-0.026-0.03420.0371-0.024236.37164.8368-6.9019
23.10210.12381.04462.4138-0.68431.707-0.04510.07210.04730.00080.10350.163-0.0186-0.0286-0.0584-0.133-0.0124-0.0243-0.13550.0181-0.07333.367820.2858-23.3624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A6 - 178
2X-RAY DIFFRACTION2{ B|* }B6 - 179

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