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- PDB-7u0v: Structure of myxoma virus M062 protein variant Lau -

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Basic information

Entry
Database: PDB / ID: 7u0v
TitleStructure of myxoma virus M062 protein variant Lau
ComponentsProbable host range protein 2-1
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 / Probable host range protein 2-1
Function and homology information
Biological speciesMyxoma virus Homo sapiens
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 myxoma virus M062 protein variant MAV
Authors: O'Byrne, P. / Khan, A.R.
History
DepositionFeb 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable host range protein 2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7092
Polymers18,6501
Non-polymers591
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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

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Components

#1: Protein Probable host range protein 2-1 / M062


Mass: 18650.213 Da / Num. of mol.: 1 / Mutation: C90S,C107S,C143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxoma virus (strain Lausanne)Homo sapiens
Strain: Lausanne / Gene: m062R / Production host: Escherichia coli (E. coli) / References: UniProt: P68550
#2: Chemical ChemComp-NI / NICKEL (II) ION


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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 50mM MgCl2 14% ethylene glycol 6% PEG8K 0.1M Tris pH 7.5

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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 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→82.123 Å / % possible obs: 99.55 % / Redundancy: 9.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.05385 / Rpim(I) all: 0.0184 / Rrim(I) all: 0.057 / Net I/σ(I): 23.92
Reflection shellResolution: 2.45→2.528 Å / Num. unique obs: 846 / CC1/2: 0.407

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cyw

5cyw


Resolution: 2.45→47.41 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 36.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 873 10.31 %
Rwork0.2112 7596 -
obs0.2169 8469 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.63 Å2 / Biso mean: 96.5222 Å2 / Biso min: 56.08 Å2
Refinement stepCycle: final / Resolution: 2.45→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 1 0 1271
Biso mean--117.81 --
Num. residues----156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.60340.48751260.4621279100
2.6034-2.80440.41011540.3431242100
2.8044-3.08670.36211600.2621242100
3.0867-3.53330.33511380.23621267100
3.5333-4.45160.26581510.19841276100
4.4516-47.410.20381440.1771129098
Refinement TLS params.Method: refined / Origin x: 8.5101 Å / Origin y: 34.1145 Å / Origin z: 34.3344 Å
111213212223313233
T0.6544 Å20.0031 Å20.0806 Å2-0.8433 Å20.0165 Å2--0.6976 Å2
L4.4085 °2-0.0517 °22.4249 °2-3.8595 °21.4463 °2--3.6844 °2
S0.1364 Å °0.1045 Å °-0.2541 Å °0.0466 Å °-0.3291 Å °0.2793 Å °0.1278 Å °-0.4667 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 156
2X-RAY DIFFRACTION1allB1

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