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- PDB-7om2: Thosea asigna virus RdRP domain in complex with Mg+2 -

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Basic information

Entry
Database: PDB / ID: 7om2
TitleThosea asigna virus RdRP domain in complex with Mg+2
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: 2.07 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
A: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,03412
Polymers154,2212
Non-polymers81310
Water19,9791109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein is forming a dimer as observed by size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-150 kcal/mol
Surface area54940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.844, 149.003, 100.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1109 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 19% PEG 3350, 0.18M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.07→80.51 Å / Num. obs: 116849 / % possible obs: 94.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 29.9 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.04
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.342 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 12183 / CC1/2: 0.601 / % possible all: 99.86

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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: 2.07→80.51 Å / SU ML: 0.2086 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 5631 4.82 %
Rwork0.1718 111218 -
obs0.1733 116849 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.61 Å2
Refinement stepCycle: LAST / Resolution: 2.07→80.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10457 0 43 1109 11609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810739
X-RAY DIFFRACTIONf_angle_d0.94314546
X-RAY DIFFRACTIONf_chiral_restr0.05371584
X-RAY DIFFRACTIONf_plane_restr0.00711875
X-RAY DIFFRACTIONf_dihedral_angle_d14.96273989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.090.31072080.25763853X-RAY DIFFRACTION99.83
2.09-2.120.28911900.24933875X-RAY DIFFRACTION99.93
2.12-2.140.28962080.23793886X-RAY DIFFRACTION99.85
2.14-2.170.28121960.22763869X-RAY DIFFRACTION99.75
2.17-2.20.2921730.2193874X-RAY DIFFRACTION99.78
2.2-2.220.2561380.21572574X-RAY DIFFRACTION87.01
2.27-2.290.26051790.21492994X-RAY DIFFRACTION98.66
2.29-2.330.26081910.19963914X-RAY DIFFRACTION99.61
2.33-2.370.24991870.19823892X-RAY DIFFRACTION99.71
2.37-2.410.24511930.19143866X-RAY DIFFRACTION99.75
2.41-2.450.24461940.19113897X-RAY DIFFRACTION99.8
2.45-2.50.23911790.19173896X-RAY DIFFRACTION99.73
2.5-2.550.24162000.18443895X-RAY DIFFRACTION99.78
2.55-2.610.25931910.18143892X-RAY DIFFRACTION99.78
2.61-2.670.23282000.17953880X-RAY DIFFRACTION99.73
2.67-2.730.21422030.18713895X-RAY DIFFRACTION99.85
2.73-2.810.23522090.1963927X-RAY DIFFRACTION99.81
2.81-2.890.2221950.18573861X-RAY DIFFRACTION99.66
2.89-2.980.20651920.17163911X-RAY DIFFRACTION99.51
2.98-3.090.22272040.17223921X-RAY DIFFRACTION99.4
3.09-3.210.20841870.17463915X-RAY DIFFRACTION99.61
3.21-3.360.19692140.16793905X-RAY DIFFRACTION99.59
3.36-3.540.19281910.16623919X-RAY DIFFRACTION99.4
3.54-3.760.18241890.14693917X-RAY DIFFRACTION98.87
3.76-4.050.16482060.1383924X-RAY DIFFRACTION99.18
4.05-4.460.15342100.13373929X-RAY DIFFRACTION99.04
4.46-5.10.16151890.13623973X-RAY DIFFRACTION98.88
5.1-6.430.17951920.17094028X-RAY DIFFRACTION99.06
6.43-80.510.16942230.17284136X-RAY DIFFRACTION98.6
Refinement TLS params.Method: refined / Origin x: 25.2522816818 Å / Origin y: -31.2313208633 Å / Origin z: -73.4543215453 Å
111213212223313233
T0.185686311054 Å20.0184213203439 Å20.00340741541255 Å2-0.174787481915 Å2-0.0121275493303 Å2--0.205989819039 Å2
L0.06706154574 °20.0543894827677 °2-0.0245860017376 °2-0.0310176234703 °2-0.0382548717801 °2--0.233994376221 °2
S0.0101599298941 Å °0.00215097503375 Å °-0.0114721978299 Å °-0.00157691030151 Å °0.00348061971206 Å °-0.00149871923297 Å °-0.022769076465 Å °-0.00480728125612 Å °-2.79745568522E-12 Å °
Refinement TLS groupSelection details: all

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