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- PDB-3g80: Nodamura virus protein b2, RNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 3g80
TitleNodamura virus protein b2, RNA-binding domain
ComponentsProtein B2
KeywordsVIRAL PROTEIN / RNA-binding / suppressor of RNAi / RNA interference
Function / homologyESAT-6-like / Helix Hairpins / RNA binding / Orthogonal Bundle / Mainly Alpha / Protein B2
Function and homology information
Biological speciesNodamura virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKorber, S. / Shaik Syed Ali, P. / Chen, J.C.
CitationJournal: Biochemistry / Year: 2009
Title: Structure of the RNA-Binding Domain of Nodamura Virus Protein B2, a Suppressor of RNA Interference.
Authors: Korber, S. / Shaik Syed Ali, P. / Chen, J.C.
History
DepositionFeb 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein B2
B: Protein B2


Theoretical massNumber of molelcules
Total (without water)22,2742
Polymers22,2742
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-26 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.190, 56.600, 98.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein B2


Mass: 11136.767 Da / Num. of mol.: 2 / Fragment: RNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nodamura virus / Gene: B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9IMM3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 3, 2008
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→500 Å / Num. all: 6658 / Num. obs: 6576 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.428 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B9Z.pdb

2b9z


Resolution: 2.5→500 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 367 5.5 %random
Rwork0.233 ---
obs0.233 6576 98.8 %-
all-6658 --
Solvent computationBsol: 69.78 Å2
Displacement parametersBiso max: 67.87 Å2 / Biso mean: 34.016 Å2 / Biso min: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.572 Å20 Å20 Å2
2--0.2 Å20 Å2
3---9.372 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.5→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 0 81 1223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.165
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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