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- PDB-6auk: Crystal structure of rotavirus Non Structural protein 2 (NSP2) mu... -

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Basic information

Entry
Database: PDB / ID: 6auk
TitleCrystal structure of rotavirus Non Structural protein 2 (NSP2) mutant S313D
ComponentsNon-structural protein 2
KeywordsVIRAL PROTEIN / Virus factory / phosphorylation / rotavirus / NSP2
Function / homology
Function and homology information


nucleoside diphosphate kinase activity / viral genome replication / ribonucleoside triphosphate phosphatase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Rotavirus NSP2 fragment, C-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / Rotavirus NSP2, N-terminal / Rotavirus NSP2, C-terminal / : / : / Rotavirus non-structural protein 35, C-terminal / Rotavirus non-structural protein 35, N-terminal / Rotavirus non-structural protein 2 ...Rotavirus NSP2 fragment, C-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / Rotavirus NSP2, N-terminal / Rotavirus NSP2, C-terminal / : / : / Rotavirus non-structural protein 35, C-terminal / Rotavirus non-structural protein 35, N-terminal / Rotavirus non-structural protein 2 / HIT family, subunit A / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 2 / Non-structural protein 2
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsHu, L. / Prasad, B.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI 36040 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080656 United States
Welch FoundationQ1279 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories.
Authors: Criglar, J.M. / Anish, R. / Hu, L. / Crawford, S.E. / Sankaran, B. / Prasad, B.V.V. / Estes, M.K.
History
DepositionSep 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7783
Polymers36,6461
Non-polymers1322
Water1,63991
1
A: Non-structural protein 2
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)294,22224
Polymers293,1708
Non-polymers1,05216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_557-x,y,-z+21
crystal symmetry operation6_557x,-y,-z+21
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_557-y,-x,-z+21
Buried area22680 Å2
ΔGint-290 kcal/mol
Surface area115370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.926, 107.926, 152.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

#1: Protein Non-structural protein 2


Mass: 36646.266 Da / Num. of mol.: 1 / Mutation: S313D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Gene: NSP2 / Production host: Escherichia coli (E. coli)
References: UniProt: A2T3N6, UniProt: A2T3P0*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM lithium sulfate, 100 mM sodium citrate, pH5.5, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2015
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14160 / % possible obs: 100 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.038 / Net I/σ(I): 23.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 17.8 % / Rmerge(I) obs: 1.333 / Num. unique obs: 702 / CC1/2: 0.662 / Rpim(I) all: 0.326 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000v715data scaling
SCALEPACK7.0.043data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9V

1l9v


Resolution: 2.603→46.016 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.2458 769 5.43 %
Rwork0.2059 --
obs0.2082 14160 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.603→46.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 6 91 2645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072606
X-RAY DIFFRACTIONf_angle_d0.8743520
X-RAY DIFFRACTIONf_dihedral_angle_d7.0441581
X-RAY DIFFRACTIONf_chiral_restr0.048392
X-RAY DIFFRACTIONf_plane_restr0.007446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6026-2.80360.37641240.29052613X-RAY DIFFRACTION98
2.8036-3.08570.33141330.26392665X-RAY DIFFRACTION100
3.0857-3.5320.26521580.22022644X-RAY DIFFRACTION100
3.532-4.44940.2221630.18212680X-RAY DIFFRACTION100
4.4494-46.0230.20551910.17392789X-RAY DIFFRACTION100

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