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Open data
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Basic information
Entry | Database: PDB / ID: 6m40 | ||||||
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Title | Crystal structure of the NS3-like helicase from Alongshan virus | ||||||
![]() | NS3-like protein | ||||||
![]() | VIRAL PROTEIN / MS3 / helicase / ALSV / Flavivirus | ||||||
Function / homology | ![]() virion component => GO:0044423 / membrane => GO:0016020 / RNA helicase activity / RNA helicase / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, X.P. / Zhu, K.X. / Chen, P. / Wojdyla, J.A. / Wang, M. / Cui, S. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.9 KB | Display | ![]() |
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PDB format | ![]() | 122.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427 KB | Display | ![]() |
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Full document | ![]() | 436.5 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55212.875 Da / Num. of mol.: 1 / Fragment: RNA helicase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion Details: 0.16 M calcium acetate, 20% (v/v) PEG3350 and 5mM TECP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.33 Å2 / Biso mean: 86.1011 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.89→47.87 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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