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- PDB-6ff0: Ryegrass mottle virus serine protease domain fused with VPg domain -

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Basic information

Entry
Database: PDB / ID: 6ff0
TitleRyegrass mottle virus serine protease domain fused with VPg domain
ComponentsSerine protease domain fused with VPg domain
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 / RNA-dependent RNA polymerase activity / nucleotide binding / 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: 2.1 Å
AuthorsKalnins, G.
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
DepositionJan 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Serine protease domain fused with VPg domain


Theoretical massNumber of molelcules
Total (without water)29,5091
Polymers29,5091
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.940, 67.520, 74.080
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 Serine protease domain fused with VPg domain


Mass: 29509.355 Da / Num. of mol.: 1 / Fragment: UNP residues 119-393
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.: 51 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M MIB, pH 9.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.96411 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96411 Å / Relative weight: 1
ReflectionResolution: 2.1→74.08 Å / Num. obs: 11945 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1699 / CC1/2: 0.924 / Rpim(I) all: 0.17 / Rrim(I) all: 0.417 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZYO

1zyo


Resolution: 2.1→49.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23481 591 5 %RANDOM
Rwork0.17319 ---
obs0.17623 11317 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.683 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2--0.26 Å2-0 Å2
3----2.08 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 0 51 1484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191461
X-RAY DIFFRACTIONr_bond_other_d00.021399
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9591981
X-RAY DIFFRACTIONr_angle_other_deg3.80333239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.4523.19147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83215241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.773158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211610
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02278
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8822.952777
X-RAY DIFFRACTIONr_mcbond_other2.872.947776
X-RAY DIFFRACTIONr_mcangle_it4.0064.392966
X-RAY DIFFRACTIONr_mcangle_other4.0094.397967
X-RAY DIFFRACTIONr_scbond_it3.8373.379684
X-RAY DIFFRACTIONr_scbond_other3.823.367682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6894.8591015
X-RAY DIFFRACTIONr_long_range_B_refined7.37234.8271548
X-RAY DIFFRACTIONr_long_range_B_other7.33734.8371546
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 42 -
Rwork0.199 837 -
obs--99.89 %

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