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- PDB-3cm3: High Resolution Crystal Structure of the Vaccinia Virus Dual-Spec... -

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Basic information

Entry
Database: PDB / ID: 3cm3
TitleHigh Resolution Crystal Structure of the Vaccinia Virus Dual-Specificity Phosphatase VH1
ComponentsDual specificity protein phosphatase
KeywordsHYDROLASE / Dual-specificity phosphatase / Vaccinia virus / VH1 / Late Protein / Protein phosphatase
Function / homology
Function and homology information


MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / negative regulation of MAPK cascade / protein serine/threonine phosphatase activity / phosphatase activity / dephosphorylation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein-tyrosine-phosphatase ...MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / negative regulation of MAPK cascade / protein serine/threonine phosphatase activity / phosphatase activity / dephosphorylation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein-tyrosine-phosphatase / virion component / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / cytoplasm
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 / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...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 / 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
BETA-MERCAPTOETHANOL / PHOSPHATE ION / Dual specificity protein phosphatase OPG106
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsKoksal, A.C. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Dimeric Quaternary Structure of the Prototypical Dual Specificity Phosphatase VH1.
Authors: Koksal, A.C. / Nardozzi, J.D. / Cingolani, G.
History
DepositionMar 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5144
Polymers20,2621
Non-polymers2513
Water5,405300
1
A: Dual specificity protein phosphatase
hetero molecules

A: Dual specificity protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0278
Polymers40,5252
Non-polymers5026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3230 Å2
ΔGint-42 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.816, 38.690, 134.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1243-

HOH

21A-1325-

HOH

31A-1373-

HOH

DetailsOne copy of the biologically relevant monomer is present in the asymmetric unit

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Components

#1: Protein Dual specificity protein phosphatase / Late protein H1


Mass: 20262.455 Da / Num. of mol.: 1 / Mutation: C110S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve / WR / Gene: H1 ORF / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P07239, protein-tyrosine-phosphatase, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 297 K / Method: batch / pH: 8
Details: 62% PEG 400, 0.1M Tris pH 8 , Batch, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC Q-270 / Detector: CCD / Date: Oct 20, 2007
Details: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block. Rh-coated Si mirror for vertical focusing.
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.32→20 Å / Num. all: 39499 / Num. obs: 35905 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.7 % / Biso Wilson estimate: 19.326 Å2 / Rsym value: 0.057 / Net I/σ(I): 65.6
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3868 / Rsym value: 0.357 / % possible all: 51.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2RF6

2rf6


Resolution: 1.32→14.11 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.057 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.18458 1800 5 %RANDOM
Rwork0.17098 ---
all0.1717 37455 --
obs0.1717 33998 90.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.352 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.32→14.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 13 300 1679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221411
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9761916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51323.93461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10915254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.492157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021049
X-RAY DIFFRACTIONr_nbd_refined0.2570.2724
X-RAY DIFFRACTIONr_nbtor_refined0.320.2978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.2215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.240
X-RAY DIFFRACTIONr_mcbond_it2.1581.5853
X-RAY DIFFRACTIONr_mcangle_it3.81921398
X-RAY DIFFRACTIONr_scbond_it3.7393558
X-RAY DIFFRACTIONr_scangle_it6.0644.5515
LS refinement shellResolution: 1.32→1.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 65 -
Rwork0.362 1248 -
obs-1250 46.1 %

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