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- PDB-1l9v: Non Structural protein encoded by gene segment 8 of rotavirus (NS... -

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Basic information

Entry
Database: PDB / ID: 1l9v
TitleNon Structural protein encoded by gene segment 8 of rotavirus (NSP2), an NTPase, ssRNA binding and nucleic acid helix-destabilizing protein
ComponentsRotavirus-NSP2
KeywordsVIRAL PROTEIN / alpha/beta protein / HIT-like fold / Octamer / Two domain protein
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 / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJayaram, H. / Taraporewala, Z. / Patton, J.T. / Prasad, B.V.
CitationJournal: Nature / Year: 2002
Title: Rotavirus protein involved in genome replication and packaging exhibits a HIT-like fold.
Authors: Jayaram, H. / Taraporewala, Z. / Patton, J.T. / Prasad, B.V.
History
DepositionMar 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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: Rotavirus-NSP2


Theoretical massNumber of molelcules
Total (without water)36,6181
Polymers36,6181
Non-polymers00
Water181
1
A: Rotavirus-NSP2
x 8


Theoretical massNumber of molelcules
Total (without water)292,9468
Polymers292,9468
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area19910 Å2
ΔGint-63 kcal/mol
Surface area117150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.432, 108.432, 152.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsOctamer - obtained by applying I422 symmtery

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Components

#1: Protein Rotavirus-NSP2


Mass: 36618.258 Da / Num. of mol.: 1 / Fragment: NSP2 of Rotavirus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian 11 rotavirus (serotype 3 / strain SA11-Ramig)
Species: Rotavirus A / Strain: SA11-Ramig / Gene: gene segment 8 / Plasmid: pQe60 (Qiagen) / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP5] / References: UniProt: Q03243
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 15% Peg 6000, 0.2 M Magnesium acetate, 0.1M Tris-HCl. Protein buffer 0.2M MgCl2, 0.5 mM EDTA , 0.5 mM DTT, 2mM Tris-HCl pH7.2. 0.2 M MgCl2 was necessary to make protein monodisperse. Protein: ...Details: 15% Peg 6000, 0.2 M Magnesium acetate, 0.1M Tris-HCl. Protein buffer 0.2M MgCl2, 0.5 mM EDTA , 0.5 mM DTT, 2mM Tris-HCl pH7.2. 0.2 M MgCl2 was necessary to make protein monodisperse. Protein:precipitant ratio 1:1. Plate like crystals (0.08 mm X 0.2 mm X 0.2 mm)Crystals grew in two to three weeks, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16-8 mg/mlprotein1drop
212-15 %peg61reservoir
30.2 Mmagnesium acetate1reservoir
4100 mMTris-HCl1reservoirpH6.5-7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2001 / Details: Mirrors
RadiationMonochromator: Two crystal monochromator (non-dispersive geometry) with Si(111) crystals
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 14403 / Num. obs: 75176 / % possible obs: 92.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.69 Å / % possible all: 94.2
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 40 Å / % possible obs: 95.9 %
Reflection shell
*PLUS
% possible obs: 94.2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→38.34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 196804.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS_PARAM Files
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1347 10.1 %RANDOM
Rwork0.241 ---
all0.241 14403 --
obs0.241 13324 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.3326 Å2 / ksol: 0.357545 e/Å3
Displacement parametersBiso mean: 54.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2---1.91 Å20 Å2
3---3.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 0 1 2546
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it9.531.5
X-RAY DIFFRACTIONc_mcangle_it14.772
X-RAY DIFFRACTIONc_scbond_it10.392
X-RAY DIFFRACTIONc_scangle_it152.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 221 10.7 %
Rwork0.335 1839 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.24 / Rfactor Rfree: 0.2884 / Rfactor Rwork: 0.24 / Highest resolution: 2.6 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_bond_d0.0071
LS refinement shell
*PLUS
Rfactor obs: 0.335

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