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- PDB-6s5i: Structure of the Lausanne variant of myxoma virus M062 protein -

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Basic information

Entry
Database: PDB / ID: 6s5i
TitleStructure of the Lausanne variant of myxoma virus M062 protein
ComponentsM62R
KeywordsVIRAL PROTEIN / myxoma virus / M062 / SAMD9 / C7L superfamily / host-range factor / innate immunity / viral antagonism
Function / homologyPoxvirus C7/F8A / Poxvirus C7/F8A protein / viral process / NICKEL (II) ION / M062R
Function and homology information
Biological speciesMyxoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsO'Byrne, P. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation IrelandSFI 12/1A/1239 Ireland
CitationJournal: To Be Published
Title: Structure of the Lausanne variant of myxoma virus M062 protein
Authors: O'Byrne, P. / Khan, A.R.
History
DepositionJul 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: M62R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7092
Polymers18,6501
Non-polymers591
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-8 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.827, 94.827, 44.136
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein M62R


Mass: 18650.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxoma virus / Gene: m062R, m062R, MYXV_gp066
Production host: Escherichia coli str. 'clone D i2' (bacteria)
References: UniProt: B2CWG9
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 7.5 50 mM CaCl2 6 - 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→47.41 Å / Num. obs: 8422 / % possible obs: 99.55 % / Redundancy: 9.8 % / Biso Wilson estimate: 84.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05385 / Rpim(I) all: 0.01841 / Rrim(I) all: 0.057 / Net I/σ(I): 23.92
Reflection shellResolution: 2.45→2.538 Å / Num. unique obs: 846 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cz3

3cz3


Resolution: 2.45→47.41 Å / SU ML: 0.3519 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 36.275
RfactorNum. reflection% reflection
Rfree0.2659 873 10.31 %
Rwork0.2112 --
obs0.2169 8469 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 96.52 Å2
Refinement stepCycle: LAST / Resolution: 2.45→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 1 0 1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141295
X-RAY DIFFRACTIONf_angle_d1.80291748
X-RAY DIFFRACTIONf_chiral_restr0.1089197
X-RAY DIFFRACTIONf_plane_restr0.0075215
X-RAY DIFFRACTIONf_dihedral_angle_d16.0517484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.60.48751260.462127999.72
2.6-2.80.41011540.343124299.64
2.8-3.090.36211600.262124299.93
3.09-3.530.33511380.23621267100
3.53-4.450.26581510.19841276100
4.450.20381440.1771129098.08
Refinement TLS params.Method: refined / Origin x: 8.51005377608 Å / Origin y: 34.1144657168 Å / Origin z: 34.3344084394 Å
111213212223313233
T0.654352459791 Å20.00313330300751 Å20.0805882153363 Å2-0.843348719496 Å20.0164530742859 Å2--0.697562037253 Å2
L4.40852193895 °2-0.0517002356538 °22.42489769022 °2-3.8595020142 °21.44625202889 °2--3.68444385237 °2
S0.136391623929 Å °0.104541592395 Å °-0.254082843463 Å °0.0465908980171 Å °-0.329132720103 Å °0.279264076393 Å °0.127813302456 Å °-0.466745928694 Å °-9.05810111537E-5 Å °
Refinement TLS groupSelection details: all

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