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- PDB-5dil: Crystal structure of the effector domain of the NS1 protein from ... -

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Basic information

Entry
Database: PDB / ID: 5dil
TitleCrystal structure of the effector domain of the NS1 protein from influenza virus B
ComponentsNon-structural protein 1
KeywordsRNA-binding Protein / Viral Protein / effector domain / RNA binding
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / symbiont-mediated suppression of host ISG15-protein conjugation / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / RNA binding
Similarity search - Function
Influenza B non-structural protein (NS1) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding
Similarity search - Domain/homology
IODIDE ION / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.01 Å
AuthorsGuan, R. / Hamilton, K. / Ma, L. / Montelione, G.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2016
Title: A Second RNA-Binding Site in the NS1 Protein of Influenza B Virus.
Authors: Ma, L.C. / Guan, R. / Hamilton, K. / Aramini, J.M. / Mao, L. / Wang, S. / Krug, R.M. / Montelione, G.T.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,67115
Polymers32,0222
Non-polymers1,65013
Water3,603200
1
A: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0269
Polymers16,0111
Non-polymers1,0158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6456
Polymers16,0111
Non-polymers6355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.689, 41.666, 49.681
Angle α, β, γ (deg.)68.72, 82.83, 78.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Non-structural protein 1 / NS1 / NS1B


Mass: 16010.823 Da / Num. of mol.: 2 / Fragment: UNP residues 141-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (B/Singapore/DSO_090134/2004)
Strain: B/Singapore/DSO_090134/2004 / Gene: NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: X2C382
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2M KI 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→46.22 Å / Num. obs: 16041 / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.22

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→28.079 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 1579 10.04 %
Rwork0.1936 --
obs0.1986 14131 94.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→28.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 13 200 2390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032216
X-RAY DIFFRACTIONf_angle_d0.7752982
X-RAY DIFFRACTIONf_dihedral_angle_d12.234858
X-RAY DIFFRACTIONf_chiral_restr0.051336
X-RAY DIFFRACTIONf_plane_restr0.002396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0088-2.03870.30491240.23961206X-RAY DIFFRACTION87
2.0387-2.07060.29771480.22561178X-RAY DIFFRACTION92
2.0706-2.10450.30131260.20681233X-RAY DIFFRACTION93
2.1045-2.14080.2761370.21221195X-RAY DIFFRACTION93
2.1408-2.17970.29741460.22131259X-RAY DIFFRACTION92
2.1797-2.22160.2421190.21881209X-RAY DIFFRACTION93
2.2216-2.26690.29151460.19921243X-RAY DIFFRACTION93
2.2669-2.31620.26551530.20171251X-RAY DIFFRACTION95
2.3162-2.37010.28781190.20441249X-RAY DIFFRACTION94
2.3701-2.42930.26061420.20751252X-RAY DIFFRACTION95
2.4293-2.49490.32371600.21351189X-RAY DIFFRACTION94
2.4949-2.56830.24621500.19831244X-RAY DIFFRACTION95
2.5683-2.65110.26891220.19791288X-RAY DIFFRACTION95
2.6511-2.74580.31261370.19681248X-RAY DIFFRACTION94
2.7458-2.85570.25691330.22021290X-RAY DIFFRACTION96
2.8557-2.98550.3011540.20611227X-RAY DIFFRACTION95
2.9855-3.14270.22441360.2061285X-RAY DIFFRACTION96
3.1427-3.33930.20991490.18921249X-RAY DIFFRACTION96
3.3393-3.59660.18361400.15971251X-RAY DIFFRACTION96
3.5966-3.95770.20771470.16581277X-RAY DIFFRACTION96
3.9577-4.52830.19111340.1631306X-RAY DIFFRACTION98
4.5283-5.69740.20621410.19791289X-RAY DIFFRACTION97
5.6974-28.08120.24871410.20211291X-RAY DIFFRACTION97

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