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- PDB-6m40: Crystal structure of the NS3-like helicase from Alongshan virus -

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Basic information

Entry
Database: PDB / ID: 6m40
TitleCrystal structure of the NS3-like helicase from Alongshan virus
ComponentsNS3-like protein
KeywordsVIRAL PROTEIN / MS3 / helicase / ALSV / Flavivirus
Function / homology
Function and homology information


virion component => GO:0044423 / RNA helicase activity / membrane => GO:0016020 / RNA helicase / ATP binding
Similarity search - Function
DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesAlongshan virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 Å
AuthorsGao, X.P. / Zhu, K.X. / Chen, P. / Wojdyla, J.A. / Wang, M. / Cui, S.
CitationJournal: Iucrj / Year: 2020
Title: Crystal structure of the NS3-like helicase from Alongshan virus.
Authors: Gao, X. / Zhu, K. / Wojdyla, J.A. / Chen, P. / Qin, B. / Li, Z. / Wang, M. / Cui, S.
History
DepositionMar 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3-like protein


Theoretical massNumber of molelcules
Total (without water)55,2131
Polymers55,2131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18760 Å2
Unit cell
Length a, b, c (Å)42.875, 58.674, 191.466
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 NS3-like protein


Mass: 55212.875 Da / Num. of mol.: 1 / Fragment: RNA helicase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alongshan virus / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A344X2I9
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: 0.16 M calcium acetate, 20% (v/v) PEG3350 and 5mM TECP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.89→47.87 Å / Num. obs: 20593 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.05 % / Biso Wilson estimate: 74.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.179 / Rrim(I) all: 0.193 / Χ2: 0.95 / Net I/σ(I): 9.68
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 6.79 % / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 3256 / CC1/2: 0.75 / Rrim(I) all: 1.55 / Χ2: 0.75 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.89→47.87 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.29
RfactorNum. reflection% reflection
Rfree0.2939 935 4.54 %
Rwork0.2463 --
obs0.2485 20578 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 187.33 Å2 / Biso mean: 86.1011 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.89→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 0 0 2995
Num. residues----379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-3.050.40491180.33292757287596
3.05-3.240.33681220.31442770289299
3.24-3.490.31571320.309328312963100
3.49-3.840.29671620.255328312993100
3.84-4.390.28061470.229628022949100
4.39-5.530.32741230.22152827295099
5.54-47.870.24761310.22032825295699

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