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- PDB-2r8f: Crystal structure of H225A NSP2 and ATP-gS complex -

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Basic information

Entry
Database: PDB / ID: 2r8f
TitleCrystal structure of H225A NSP2 and ATP-gS complex
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Non-structural protein 2
Similarity search - Component
Biological speciesSimian 11 rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,1693
Polymers36,5511
Non-polymers6182
Water1,78399
1
A: Non-structural RNA-binding protein 35
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)297,35524
Polymers292,4108
Non-polymers4,94616
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 area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.644, 108.644, 155.664
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: 36551.191 Da / Num. of mol.: 1 / Mutation: H225A
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: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
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 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9790903 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9790903 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 11836 / Num. obs: 11744 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.81 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.97 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1151 / % possible all: 100

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Processing

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

1l9v


Resolution: 2.8→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 838 -random
Rwork0.2163 ---
all0.218 11836 --
obs-11718 99 %-
Displacement parametersBiso mean: 43.6 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 36 99 2632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006927
X-RAY DIFFRACTIONc_angle_deg1.24

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