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- PDB-7u0w: Structure of myxoma virus M062 protein variant MAV -

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Basic information

Entry
Database: PDB / ID: 7u0w
TitleStructure of myxoma virus M062 protein variant MAV
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 / Probable host range protein 2-1
Function and homology information
Biological speciesMyxoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.205 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 / Database references ...Data collection / Database references / Refinement description / 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 / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
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
B: Probable host range protein 2-1


Theoretical massNumber of molelcules
Total (without water)37,2762
Polymers37,2762
Non-polymers00
Water0
1
A: Probable host range protein 2-1


Theoretical massNumber of molelcules
Total (without water)18,6381
Polymers18,6381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable host range protein 2-1


Theoretical massNumber of molelcules
Total (without water)18,6381
Polymers18,6381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.844, 148.844, 38.596
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 3 through 145)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 3 - 145 / Label seq-ID: 6 - 148

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 3 through 145)AA
2chain BBB

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Components

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


Mass: 18638.160 Da / Num. of mol.: 2 / Mutation: I79T,C90S,C107S,C143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxoma virus (strain Lausanne) / Strain: Lausanne / Gene: m062R / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P68550

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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: 3.31 Å3/Da / Density % sol: 62.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 100mM Imidazole, pH 8.0 11-14% PEG 3,350

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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: 3.2→128.9 Å / % possible obs: 99.7 % / Redundancy: 9.7 % / Biso Wilson estimate: 149.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.02 / Rrim(I) all: 0.061 / Net I/σ(I): 31.9
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.551 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1441 / CC1/2: 0.624 / Rpim(I) all: 0.508 / Rrim(I) all: 1.633 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cz3

5cz3


Resolution: 3.205→74.422 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 41.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3072 392 4.73 %
Rwork0.2888 7904 -
obs0.2897 8296 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.33 Å2 / Biso mean: 146.2332 Å2 / Biso min: 105.13 Å2
Refinement stepCycle: final / Resolution: 3.205→74.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 0 0 2313
Num. residues----287
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1234X-RAY DIFFRACTION22.299TORSIONAL
12B1234X-RAY DIFFRACTION22.299TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.205-3.66870.39051240.3762255999
3.6687-4.62210.34421330.32392619100
4.6221-74.4220.28361350.26452726100
Refinement TLS params.Method: refined / Origin x: 4.2212 Å / Origin y: -57.8282 Å / Origin z: -0.0525 Å
111213212223313233
T1.2333 Å20.0716 Å2-0.1619 Å2-1.2816 Å2-0.1056 Å2--1.5604 Å2
L8.4402 °2-1.8017 °22.0002 °2--1.8572 °2-1.1214 °2---0.1759 °2
S-0.3598 Å °-0.1099 Å °0.5157 Å °0.073 Å °0.3293 Å °-0.125 Å °-0.2329 Å °-0.0091 Å °0.0868 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 146
2X-RAY DIFFRACTION1allB3 - 145

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