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- PDB-9ogq: Rotavirus NSP2 K294E mutant -

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Basic information

Entry
Database: PDB / ID: 9ogq
TitleRotavirus NSP2 K294E mutant
ComponentsNon-structural protein 2
KeywordsVIRAL PROTEIN / Rotavirus / NSP2 / viral factory
Function / homology
Function and homology information


nucleoside diphosphate kinase activity / ribonucleoside triphosphate phosphatase activity / viral genome replication / 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, 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
Similarity search - Domain/homology
Non-structural protein 2
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHollis, T.J. / Nichols, S.L. / Esstman, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateDM United States
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2025
Title: K294E change in the rotavirus factory forming protein NSP2 stabilizes a rare C-terminal conformation.
Authors: Nichols, S.L. / Hollis, T. / Salsbury, F.R. / Esstman, S.M.
History
DepositionMay 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)36,2351
Polymers36,2351
Non-polymers00
Water3,477193
1
A: Non-structural protein 2
x 8


Theoretical massNumber of molelcules
Total (without water)289,8788
Polymers289,8788
Non-polymers00
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_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)108.426, 108.426, 153.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Non-structural protein 2 / NSP2 / NCVP3 / Non-structural RNA-binding protein 35 / NS35


Mass: 36234.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Strain: SA11 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q03243, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl pH 7.5, 0.2M MgAc, 12% PEG6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 15, 2024 / Details: varimax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 42005 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.032 / Rrim(I) all: 0.116 / Χ2: 1.08 / Net I/σ(I): 6.8 / Num. measured all: 549241
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.25-2.3212.21.935160.7890.9390.5671.9831.268100
2.32-2.3912.81.07534400.8960.9720.3131.121.099100
2.39-2.4813.10.85535330.930.9820.2460.891.125100
2.48-2.5813.50.79634630.9580.9890.2250.8281.017100
2.58-2.6913.80.48434850.9750.9940.1350.5031.046100
2.69-2.83140.34734960.9870.9970.0960.3611.031100
2.83-3.0113.90.23335140.9920.9980.0650.2421.143100
3.01-3.2413.90.15134810.9960.9990.0420.1571.093100
3.24-3.5713.70.08134940.99910.0230.0851.076100
3.57-4.0913.40.05635100.99910.0160.0581.068100
4.09-5.1511.60.04335230.99910.0130.0451.084100
5.15-5011.20.0323550110.010.0330.999.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→46.39 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 1137 5.18 %
Rwork0.2267 --
obs0.228 21936 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 0 193 2712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.663
X-RAY DIFFRACTIONf_dihedral_angle_d4.846331
X-RAY DIFFRACTIONf_chiral_restr0.04389
X-RAY DIFFRACTIONf_plane_restr0.005438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.38261670.35382582X-RAY DIFFRACTION95
2.3-2.420.3968990.33282563X-RAY DIFFRACTION92
2.42-2.570.37541290.34112524X-RAY DIFFRACTION91
2.57-2.770.34741460.30582465X-RAY DIFFRACTION89
2.77-3.050.31591440.2662414X-RAY DIFFRACTION88
3.05-3.490.26811250.23892623X-RAY DIFFRACTION92
3.49-4.40.20151700.17542701X-RAY DIFFRACTION97
4.4-46.390.18821570.17432927X-RAY DIFFRACTION98

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