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- PDB-7rlm: Crystal Structure of Potato Leafroll Virus (PLRV) Coat Protein -

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Basic information

Entry
Database: PDB / ID: 7rlm
TitleCrystal Structure of Potato Leafroll Virus (PLRV) Coat Protein
ComponentsCoat protein
KeywordsVIRAL PROTEIN / PLRV / polerovirus / icosahedral virus / quasi-equivalence / viral assembly / capsid / plant virus
Function / homologyLuteovirus group 1 coat protein / Luteovirus coat protein / Viral coat protein subunit / viral capsid / structural molecule activity / BROMIDE ION / Coat protein
Function and homology information
Biological speciesPotato leafroll virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAdams, M.C. / Chappie, J.S. / Schiltz, C.J.
Funding support United States, 2items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2020-67034-31750 United States
United States Department of Agriculture (USDA)2019-05200 United States
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Crystal structure of the potato leafroll virus coat protein and implications for viral assembly.
Authors: Adams, M.C. / Schiltz, C.J. / Heck, M.L. / Chappie, J.S.
History
DepositionJul 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
B: Coat protein
A: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4967
Polymers93,4166
Non-polymers801
Water12,394688
1
B: Coat protein


Theoretical massNumber of molelcules
Total (without water)15,5691
Polymers15,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6492
Polymers15,5691
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)15,5691
Polymers15,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Coat protein


Theoretical massNumber of molelcules
Total (without water)15,5691
Polymers15,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Coat protein


Theoretical massNumber of molelcules
Total (without water)15,5691
Polymers15,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Coat protein


Theoretical massNumber of molelcules
Total (without water)15,5691
Polymers15,5691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.863, 67.479, 75.887
Angle α, β, γ (deg.)79.670, 76.219, 81.673
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Coat protein


Mass: 15569.415 Da / Num. of mol.: 6 / Fragment: UNP residues 68-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Potato leafroll virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76QV9
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 1.92 Å3/Da / Density % sol: 35.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane, pH 7.7, 26% PEG3350, 0.1 M sodium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.504→72.86 Å / Num. obs: 177750 / % possible obs: 89.13 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.6
Reflection shellResolution: 1.504→1.558 Å / Num. unique obs: 6323 / CC1/2: 0.315

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6SCO

6sco


Resolution: 1.8→72.86 Å / SU ML: 0.2036 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 22.5047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 3090 5.15 %
Rwork0.1672 56897 -
obs0.1698 59987 93.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.88 Å2
Refinement stepCycle: LAST / Resolution: 1.8→72.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6542 0 1 688 7231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686810
X-RAY DIFFRACTIONf_angle_d0.88629221
X-RAY DIFFRACTIONf_chiral_restr0.0571009
X-RAY DIFFRACTIONf_plane_restr0.00521181
X-RAY DIFFRACTIONf_dihedral_angle_d19.36722503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.28091240.24482589X-RAY DIFFRACTION92.82
1.83-1.860.27841350.23282691X-RAY DIFFRACTION95.09
1.86-1.890.28581610.20552578X-RAY DIFFRACTION94.45
1.89-1.920.27141270.20392688X-RAY DIFFRACTION95.13
1.92-1.960.28051400.18532613X-RAY DIFFRACTION94.9
1.96-20.23331450.18032637X-RAY DIFFRACTION94.31
2-2.050.22531420.18852664X-RAY DIFFRACTION94.19
2.05-2.090.23981260.18652544X-RAY DIFFRACTION93.78
2.09-2.150.24581420.18592616X-RAY DIFFRACTION93.91
2.15-2.20.23011400.18122488X-RAY DIFFRACTION90.37
2.2-2.270.26051590.17732633X-RAY DIFFRACTION95.29
2.27-2.340.22011250.18942682X-RAY DIFFRACTION95.57
2.34-2.420.27081730.18782629X-RAY DIFFRACTION95.18
2.42-2.520.27331470.19422591X-RAY DIFFRACTION94.84
2.52-2.640.23161320.18782644X-RAY DIFFRACTION92.94
2.64-2.780.24591470.18952478X-RAY DIFFRACTION91.4
2.78-2.950.22421270.17952517X-RAY DIFFRACTION90.09
2.95-3.180.21891460.17432594X-RAY DIFFRACTION93.01
3.18-3.50.22291470.14762495X-RAY DIFFRACTION91.48
3.5-40.15991410.132495X-RAY DIFFRACTION88.55
4-5.040.1471370.11852504X-RAY DIFFRACTION90.6
5.05-72.860.18581270.15352527X-RAY DIFFRACTION90.8

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