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- PDB-7yzv: Ryegrass mottle virus serine protease domain S159A mutant -

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Basic information

Entry
Database: PDB / ID: 7yzv
TitleRyegrass mottle virus serine protease domain S159A mutant
ComponentsRNA-directed RNA polymeraseRNA-dependent RNA polymerase
KeywordsVIRAL PROTEIN / serine protease / viral protease / viral polypeptide / viral genome-linked protein
Function / homology
Function and homology information


host cell membrane / viral RNA genome replication / nucleotide binding / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / DNA-templated transcription / proteolysis / RNA binding / membrane
Similarity search - Function
Peptidase S39B, luteovirus / Peptidase family S39 domain profile. / RNA-directed RNA polymerase, luteovirus / Viral RNA-directed RNA-polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesRyegrass mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKalnins, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/3/19/462European Union
CitationJournal: Int J Mol Sci / Year: 2023
Title: VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure.
Authors: Kalnins, G. / Ludviga, R. / Kalnciema, I. / Resevica, G. / Zeltina, V. / Bogans, J. / Tars, K. / Zeltins, A. / Balke, I.
History
DepositionFeb 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)20,8681
Polymers20,8681
Non-polymers00
Water1,78399
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)112.222, 36.950, 69.498
Angle α, β, γ (deg.)90.000, 126.291, 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
Components on special symmetry positions
IDModelComponents
11A-261-

HOH

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Components

#1: Protein RNA-directed RNA polymerase / RNA-dependent RNA polymerase


Mass: 20867.982 Da / Num. of mol.: 1 / Mutation: S159A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ryegrass mottle virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0MCW0, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.85 % / Description: Needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.18 M ammonium sulfate, 22% PEG 8000, 0.1 M sodium cacodylate (pH 6.5)

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→56.02 Å / Num. obs: 29492 / % possible obs: 95.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 15.04 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.148 / Net I/σ(I): 6.7
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4334 / CC1/2: 0.724 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.17.1_3660refinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FF0

6ff0


Resolution: 1.6→56.02 Å / SU ML: 0.2133 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2627 1399 4.75 %
Rwork0.2221 28068 -
obs0.224 29467 95.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→56.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1353 0 0 99 1452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531379
X-RAY DIFFRACTIONf_angle_d0.79791871
X-RAY DIFFRACTIONf_chiral_restr0.0583219
X-RAY DIFFRACTIONf_plane_restr0.0057236
X-RAY DIFFRACTIONf_dihedral_angle_d29.2978196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.2771230.26332813X-RAY DIFFRACTION96.71
1.65-1.720.27591370.25312821X-RAY DIFFRACTION96.54
1.72-1.80.29091330.23462723X-RAY DIFFRACTION93.12
1.8-1.890.26681480.23572811X-RAY DIFFRACTION96.48
1.89-2.010.31311520.25462792X-RAY DIFFRACTION95.96
2.01-2.170.26211500.23422758X-RAY DIFFRACTION93.93
2.17-2.380.29891510.23042792X-RAY DIFFRACTION96.02
2.38-2.730.26471340.22432841X-RAY DIFFRACTION96.5
2.73-3.440.2321260.21792866X-RAY DIFFRACTION95.47
3.44-56.020.24041450.19162851X-RAY DIFFRACTION93.51

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