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- PDB-7om9: Thosea asigna virus RdRP domain -

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Basic information

Entry
Database: PDB / ID: 7om9
TitleThosea asigna virus RdRP domain
ComponentsRNA-dependent RNA polymerase
KeywordsVIRAL PROTEIN / RdRP / polymerase
Function / homology: / : / Permutotetravirus RNA-dependent RNA polymerase palm domain / Permutotetravirus RNA-dependent RNA polymerase thumb domain / RNA-directed RNA polymerase activity / DNA/RNA polymerase superfamily / ATP binding / metal ion binding / RNA-dependent RNA polymerase
Function and homology information
Biological speciesThosea asigna virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFerrero, D.S. / Falqui, M. / Verdaguer, N.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2017-83906-P Spain
Spanish National Research Council2020AEP121 Spain
CitationJournal: Viruses / Year: 2021
Title: Snapshots of a Non-Canonical RdRP in Action.
Authors: Ferrero, D.S. / Falqui, M. / Verdaguer, N.
History
DepositionMay 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA-dependent RNA polymerase
A: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)154,2212
Polymers154,2212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein is a dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-28 kcal/mol
Surface area52330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.152, 74.438, 96.562
Angle α, β, γ (deg.)90.000, 104.648, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 77110.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thosea asigna virus / Gene: RdRp / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6A562

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate pH4.6, 0.25M (NH4)SO4, 26% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→48.52 Å / Num. obs: 29359 / % possible obs: 98.22 % / Redundancy: 4.8 % / Biso Wilson estimate: 78.86 Å2 / CC1/2: 0.941 / Rpim(I) all: 0.1552 / Rrim(I) all: 0.3546 / Net I/σ(I): 10.52
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.217 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 2956 / CC1/2: 0.514 / Rpim(I) all: 0.573 / % possible all: 99.29

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHI

4xhi


Resolution: 3→48.52 Å / SU ML: 0.4582 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.2728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2778 1385 4.72 %
Rwork0.2583 27974 -
obs0.2592 29359 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.24 Å2
Refinement stepCycle: LAST / Resolution: 3→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9776 0 0 0 9776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00399985
X-RAY DIFFRACTIONf_angle_d0.72813506
X-RAY DIFFRACTIONf_chiral_restr0.04371485
X-RAY DIFFRACTIONf_plane_restr0.00561737
X-RAY DIFFRACTIONf_dihedral_angle_d18.59693714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.110.39441440.40292806X-RAY DIFFRACTION99.29
3.11-3.230.36361460.37892790X-RAY DIFFRACTION99.19
3.23-3.380.40511380.37392789X-RAY DIFFRACTION98.62
3.38-3.560.31781340.3272755X-RAY DIFFRACTION97.73
3.56-3.780.32011460.28642784X-RAY DIFFRACTION98.62
3.78-4.070.30991250.28262784X-RAY DIFFRACTION97.58
4.07-4.480.26271560.23142747X-RAY DIFFRACTION97.61
4.48-5.130.24291390.22742781X-RAY DIFFRACTION97.59
5.13-6.460.26331230.23532847X-RAY DIFFRACTION98.18
6.46-48.520.21171340.19282891X-RAY DIFFRACTION98.12

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