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- PDB-4g0j: Crystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals S... -

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Basic information

Entry
Database: PDB / ID: 4g0j
TitleCrystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals Specific Recognition of 5'-GG Sequence for RTPase activity
ComponentsNon-structural protein 2
KeywordsHYDROLASE / RNA triphosphatase / RNA binding / hydrolase activity / nucleotide binding / metal ion binding / host cell cytoplasm
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 fragment, C-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / : / : / Rotavirus non-structural protein 35, N-terminal / Rotavirus NSP2, N-terminal / Rotavirus NSP2, C-terminal / Rotavirus non-structural protein 35, C-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 non-structural protein 35, N-terminal / Rotavirus NSP2, N-terminal / Rotavirus NSP2, C-terminal / Rotavirus non-structural protein 35, C-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
Similarity search - Component
Biological speciesSimian 11 rotavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.398 Å
AuthorsHu, L. / Prasad, B.V.V.
CitationJournal: J.Virol. / Year: 2012
Title: Crystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals Specific Recognition of 5' GG Sequence for RTPase Activity.
Authors: Hu, L. / Chow, D.C. / Patton, J.T. / Palzkill, T. / Estes, M.K. / Prasad, B.V.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Non-structural protein 2
C: Non-structural protein 2
D: Non-structural protein 2
E: Non-structural protein 2
F: Non-structural protein 2
G: Non-structural protein 2
H: Non-structural protein 2
I: Non-structural protein 2
J: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)340,70410
Polymers340,70410
Non-polymers00
Water00
1
A: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)34,0701
Polymers34,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.484, 122.484, 301.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.000792, 0.999994, 0.003422), (-0.999979, 0.00077, 0.006424), (0.006422, -0.003427, 0.999974)61.7141, 62.04994, 150.05872

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Components

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


Mass: 34070.391 Da / Num. of mol.: 10 / Mutation: C-terminal deletion mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian 11 rotavirus / Strain: SA11-Ramig G3-Px[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx / Production host: Escherichia coli (E. coli)
References: UniProt: Q03243, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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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: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate, pH 6.5, 70 mM NaCl, 1 mM EDTA, 10-12% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.299
11-H, K, -L20.701
ReflectionResolution: 3.398→301.31 Å / Num. all: 60746 / Num. obs: 60390 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 3.398→3.52 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.398→301.31 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.851 / SU B: 25.3 / SU ML: 0.396 / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29381 3107 5.1 %RANDOM
Rwork0.2369 ---
obs0.23988 57280 99.27 %-
all-60746 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.82 Å2
Baniso -1Baniso -2Baniso -3
1--35.86 Å20 Å20 Å2
2---35.86 Å20 Å2
3---71.72 Å2
Refinement stepCycle: LAST / Resolution: 3.398→301.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23600 0 0 0 23600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224110
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.94232610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22152890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76824.7831150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.62154410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.60715100
X-RAY DIFFRACTIONr_chiral_restr0.1050.23670
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117940
LS refinement shellResolution: 3.398→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 224 -
Rwork0.311 4133 -
obs--97.91 %

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