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- PDB-6uct: Crystal structure of Mal de Rio Cuarto virus P9-1 viroplasm prote... -

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Basic information

Entry
Database: PDB / ID: 6uct
TitleCrystal structure of Mal de Rio Cuarto virus P9-1 viroplasm protein (C-arm deletion mutant)
Componentsp9-1
KeywordsVIRAL PROTEIN / Fijivirus / MRCV / Wheat / Maize / Reoviridae / viroplasm
Function / homologyReovirus P9-like / Reovirus P9-like family / p9-1
Function and homology information
Biological speciesMal de Rio Cuarto virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsLlauger, G. / Klinke, S. / Monti, D. / Sycz, G. / Cerutti, M.L. / Goldbaum, F.A. / del Vas, M. / Otero, L.H.
Funding support Argentina, 4items
OrganizationGrant numberCountry
National Research Council (NRC, Argentina)PICT 2015-0621 Argentina
National Research Council (NRC, Argentina)PICT 2016-1425 Argentina
National Research Council (NRC, Argentina)PICT-2014-3754 Argentina
National Research Council (NRC, Argentina)PICT-2017-2537 Argentina
CitationJournal: To Be Published
Title: Crystal structure of Mal de Rio Cuarto virus P9-1 viroplasm protein (C-arm deletion mutant)
Authors: Llauger, G. / Klinke, S. / Monti, D. / Sycz, G. / Cerutti, M.L. / Goldbaum, F.A. / del Vas, M. / Otero, L.H.
History
DepositionSep 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: p9-1


Theoretical massNumber of molelcules
Total (without water)37,2571
Polymers37,2571
Non-polymers00
Water00
1
A: p9-1

A: p9-1


Theoretical massNumber of molelcules
Total (without water)74,5142
Polymers74,5142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)86.557, 86.557, 95.598
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein p9-1


Mass: 37256.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mal de Rio Cuarto virus / Plasmid: pET24a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D9U542

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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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 13% (w/v) PEG 8000, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2019
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.47→47.8 Å / Num. obs: 5035 / % possible obs: 99.2 % / Redundancy: 24.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.027 / Rrim(I) all: 0.136 / Net I/σ(I): 15.8
Reflection shellResolution: 3.47→3.8 Å / Redundancy: 25.6 % / Rmerge(I) obs: 2.912 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1138 / CC1/2: 0.548 / Rpim(I) all: 0.582 / Rrim(I) all: 3.013 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VJJ

3vjj


Resolution: 3.47→43.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.613
RfactorNum. reflection% reflectionSelection details
Rfree0.277 276 5.52 %RANDOM
Rwork0.22 ---
obs0.223 5004 99 %-
Displacement parametersBiso max: 281.62 Å2 / Biso mean: 185.21 Å2 / Biso min: 112.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.9738 Å20 Å20 Å2
2---0.9738 Å20 Å2
3---1.9476 Å2
Refinement stepCycle: final / Resolution: 3.47→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 0 0 2013
Num. residues----243
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d731SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes284HARMONIC5
X-RAY DIFFRACTIONt_it2049HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion269SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2354SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2049HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2759HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion22.71
LS refinement shellResolution: 3.47→3.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2735 89 6.64 %
Rwork0.2372 1252 -
all0.2395 1341 -
obs--96.54 %
Refinement TLS params.Method: refined / Origin x: 13.2924 Å / Origin y: -15.2388 Å / Origin z: -0.4668 Å
111213212223313233
T-0.0684 Å20.152 Å2-0.0123 Å2--0.0304 Å20.0741 Å2---0.1798 Å2
L7.9271 °2-2.9104 °2-1.3329 °2-5.7471 °20.5047 °2--5.7914 °2
S-0.1243 Å °-0.541 Å °-0.5442 Å °0.1089 Å °0.1491 Å °-0.3931 Å °0.5442 Å °0.5442 Å °-0.0249 Å °
Refinement TLS groupSelection details: { A|* }

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