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- PDB-2r7c: Crystallographic and biochemical analysis of rotavirus NSP2 with ... -

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Basic information

Entry
Database: PDB / ID: 2r7c
TitleCrystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals an NDP kinase like activity
ComponentsNon-structural RNA-binding protein 35
KeywordsRNA BINDING PROTEIN / Rotavirus / NDP Kinase / non structural protein / NTPase / RNA-binding
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 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
PHOSPHATE ION / Non-structural protein 2
Similarity search - Component
Biological speciesSimian 11 rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKumar, M. / Prasad, B.V.V.
Citation
Journal: J.Virol. / Year: 2007
Title: Crystallographic and Biochemical Analysis of Rotavirus NSP2 with Nucleotides Reveals a Nucleoside Diphosphate Kinase-Like Activity
Authors: Kumar, M. / Jayaram, H. / Vasquez-Del Carpio, R. / Jiang, X. / Taraporewala, Z.F. / Jacobson, R.H. / Patton, J.T. / Prasad, B.V.V.
#1: Journal: 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.V.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural RNA-binding protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8082
Polymers36,7131
Non-polymers951
Water27015
1
A: Non-structural RNA-binding protein 35
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)294,46616
Polymers293,7068
Non-polymers7608
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_465y-1,x+1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.175, 108.175, 151.924
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 RNA-binding protein 35 / NSP2 / NS35 / NCVP3


Mass: 36713.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian 11 rotavirus (serotype 3 / strain SA11-Ramig)
Species: Rotavirus A / Strain: Ramig / Gene: S8, SEGMENT 8 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q03243
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 59.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 6-8% PEG 10000, 20mM Tris-HCl pH 7.5, 10-15mM nucleotide, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979399 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2005 / Details: ADSC914_DETECTOR_DIMENSIONS=3072 3072
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979399 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 12746 / Num. obs: 12530 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.8 % / Biso Wilson estimate: 80.03688 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 14.3 / Num. unique all: 1226 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
CNS1.1refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1l9v

1l9v


Resolution: 2.7→44.06 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 833 -RANDOM
Rwork0.2255 ---
all-12746 --
obs-11690 91.7 %-
Displacement parametersBiso mean: 41.8433 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 5 15 2535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011187
X-RAY DIFFRACTIONc_angle_deg1.33635

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