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- PDB-2rf6: Crystal Structure of the Vaccinia Virus Dual-Specificity Phosphat... -

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Basic information

Entry
Database: PDB / ID: 2rf6
TitleCrystal 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
Dual specificity protein phosphatase OPG106
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKoksal, A.C. / Cingolani, G.
CitationJournal: To be Published
Title: Crystal Structure of the Vaccinia Virus Dual-Specificity Phosphatase VH1
Authors: Koksal, A.C. / Nardozzi, J.D. / Cingolani, G.
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 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 1.5Aug 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)20,3592
Polymers20,2621
Non-polymers961
Water3,099172
1
A: Dual specificity protein phosphatase
hetero molecules

A: Dual specificity protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7174
Polymers40,5252
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2610 Å2
ΔGint-66 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.638, 63.994, 135.428
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-189-

HOH

21A-249-

HOH

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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 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P07239, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 294.15 K / Method: batch / pH: 7
Details: 82% PEG 400, 0.1M MOPS pH 7.0, BATCH, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: Xcalibur / Detector: CCD / Date: Aug 18, 2007
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→6 Å / Num. all: 10692 / Num. obs: 10692 / % possible obs: 85.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 16.031 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 22.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 9.4 / Num. unique all: 1148 / Rsym value: 0.169 / % possible all: 65.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrysalisProCCDdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P4D Variola major H1 phosphatase

2p4d


Resolution: 1.95→6 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.927
Isotropic thermal model: isotropic for protein atoms and water, anisotropic for sulfate ion.
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20813 511 4.8 %RANDOM
Rwork0.18691 ---
obs0.18794 10161 87.77 %-
all-12159 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 5 172 1551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221406
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9781899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61223.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.10215263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.188158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021026
X-RAY DIFFRACTIONr_nbd_refined0.2420.2726
X-RAY DIFFRACTIONr_nbtor_refined0.3320.2953
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.218
X-RAY DIFFRACTIONr_mcbond_it2.3481.5851
X-RAY DIFFRACTIONr_mcangle_it3.40421387
X-RAY DIFFRACTIONr_scbond_it4.4293555
X-RAY DIFFRACTIONr_scangle_it6.0964.5512
LS refinement shellResolution: 1.95→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 23 -
Rwork0.228 422 -
obs-248 54.07 %

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