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- PDB-8wil: Crystal structure of Jingmen tick virus RNA-dependent RNA polymer... -

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Basic information

Entry
Database: PDB / ID: 8wil
TitleCrystal structure of Jingmen tick virus RNA-dependent RNA polymerase (D55 construct)
ComponentsJingmen tick virus NSP1
KeywordsTRANSFERASE / RNA virus / flavi-like viruses / Jingmen tick virus / RNA-dependent RNA polymerase
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesJingmen tick virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, X. / Jing, X. / Deng, F. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070185 China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase.
Authors: Wang, X. / Jing, X. / Shi, J. / Liu, Q. / Shen, S. / Cheung, P.P. / Wu, J. / Deng, F. / Gong, P.
History
DepositionSep 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Jingmen tick virus NSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,12011
Polymers100,2251
Non-polymers89510
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.519, 89.185, 121.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Jingmen tick virus NSP1


Mass: 100224.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jingmen tick virus / Strain: YN-flaviV / Gene: segment1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Rosetta
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5 / Details: magnesium chloride, HEPES pH7.5, PEG3350

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. obs: 40074 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.022 / Rrim(I) all: 0.098 / Χ2: 0.953 / Net I/σ(I): 6.4 / Num. measured all: 759365
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.1819.10.50839350.9680.9920.1190.5220.912100
2.18-2.2618.80.40139490.9780.9940.0940.4120.919100
2.26-2.3718.40.3239570.9830.9960.0760.3290.96799.9
2.37-2.4919.80.25139480.9910.9980.0580.2570.954100
2.49-2.6519.40.19439610.9940.9980.0450.20.946100
2.65-2.8518.10.14539800.9960.9990.0350.1490.96499.9
2.85-3.1419.80.10739940.9980.9990.0250.111.016100
3.14-3.5919.10.07340310.99910.0170.0751.018100
3.59-4.5219.20.05340650.99910.0120.0550.938100
4.52-6017.90.04642540.99910.0110.0470.89499.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model determined by SAD

Resolution: 2.1→46.76 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 1954 4.9 %
Rwork0.1717 --
obs0.1734 39850 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4449 0 58 383 4890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084668
X-RAY DIFFRACTIONf_angle_d0.8516322
X-RAY DIFFRACTIONf_dihedral_angle_d7.557667
X-RAY DIFFRACTIONf_chiral_restr0.049694
X-RAY DIFFRACTIONf_plane_restr0.008805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.24351400.18862652X-RAY DIFFRACTION100
2.15-2.210.25211350.17842694X-RAY DIFFRACTION100
2.21-2.280.23851500.18182664X-RAY DIFFRACTION100
2.28-2.350.24461470.18772651X-RAY DIFFRACTION100
2.35-2.430.25921380.18872669X-RAY DIFFRACTION100
2.43-2.530.22911260.17472680X-RAY DIFFRACTION100
2.53-2.650.19651350.182693X-RAY DIFFRACTION100
2.65-2.790.23051500.17692684X-RAY DIFFRACTION100
2.79-2.960.22211510.17922678X-RAY DIFFRACTION100
2.96-3.190.21891380.18372705X-RAY DIFFRACTION100
3.19-3.510.17591270.16842719X-RAY DIFFRACTION100
3.51-4.020.18031350.15312742X-RAY DIFFRACTION100
4.02-5.060.1651270.14392781X-RAY DIFFRACTION100
5.06-46.760.21021550.1882884X-RAY DIFFRACTION100

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