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- PDB-2p4d: Structure-assisted discovery of Variola major H1 phosphatase inhi... -

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Basic information

Entry
Database: PDB / ID: 2p4d
TitleStructure-assisted discovery of Variola major H1 phosphatase inhibitors
ComponentsDual specificity protein phosphatase
KeywordsHYDROLASE / dual specificity phosphatase / enzyme / small pox / drug design
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / virion component => GO:0044423 / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein-tyrosine-phosphatase / 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 / 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 H1 / Dual specificity protein phosphatase H1
Similarity search - Component
Biological speciesVariola virus (smallpox virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsPhan, J. / Tropea, J.E. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure-assisted discovery of variola major H1 phosphatase inhibitors
Authors: Phan, J. / Tropea, J.E. / Waugh, D.S.
History
DepositionMar 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software / Item: _reflns_shell.percent_possible_all / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase


Theoretical massNumber of molelcules
Total (without water)20,2351
Polymers20,2351
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.441, 101.441, 95.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-190-

HOH

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Components

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


Mass: 20235.174 Da / Num. of mol.: 1 / Fragment: Enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variola virus (smallpox virus) / Genus: Orthopoxvirus / Plasmid: pVPPase2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P33064, UniProt: P0DOQ5*PLUS, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 26% PEG MME 2000, 1.5 M KF, 3 mM Na3VO4, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792, 0.97925, 0.97939
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 5, 2005 / Details: Crystals and mirrors
RadiationMonochromator: Si-220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.979251
30.979391
ReflectionResolution: 1.8→25 Å / Num. all: 22420 / Num. obs: 22420 / % possible obs: 88.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 28.915 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5 / Num. unique all: 2239

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.744 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1155 5.2 %RANDOM
Rwork0.178 ---
obs0.179 22330 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.769 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 0 190 1506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221343
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9711816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7835162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48123.3959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.915245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.038159
X-RAY DIFFRACTIONr_chiral_restr0.1250.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02993
X-RAY DIFFRACTIONr_nbd_refined0.2080.2582
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.215
X-RAY DIFFRACTIONr_mcbond_it1.3731.5843
X-RAY DIFFRACTIONr_mcangle_it2.02721331
X-RAY DIFFRACTIONr_scbond_it3.4673573
X-RAY DIFFRACTIONr_scangle_it4.8024.5485
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 79 -
Rwork0.2 1553 -
obs-1632 97.55 %

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