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- PDB-8c9k: Structure of Mpox virus poxin -

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Basic information

Entry
Database: PDB / ID: 8c9k
TitleStructure of Mpox virus poxin
ComponentsMPXVgp165
KeywordsVIRAL PROTEIN / virus / pox / mpox / nuclease
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP binding / nuclease activity / symbiont-mediated suppression of host innate immune response
Similarity search - Function
Poxin, virus / Schlafen family / Orthopoxvirus B3 protein / Poxviridae B3 protein / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2
Similarity search - Domain/homology
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsDuchoslav, V. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Mpox virus poxin
Authors: Duchoslav, V. / Boura, E.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MPXVgp165
B: MPXVgp165
C: MPXVgp165
D: MPXVgp165


Theoretical massNumber of molelcules
Total (without water)90,0404
Polymers90,0404
Non-polymers00
Water15,763875
1
A: MPXVgp165
B: MPXVgp165


Theoretical massNumber of molelcules
Total (without water)45,0202
Polymers45,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-8 kcal/mol
Surface area18410 Å2
MethodPISA
2
C: MPXVgp165

D: MPXVgp165


Theoretical massNumber of molelcules
Total (without water)45,0202
Polymers45,0202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_453-x-1,y+1/2,-z-21
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.430, 94.130, 94.670
Angle α, β, γ (deg.)90.000, 105.260, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
MPXVgp165


Mass: 22509.893 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: MPXV-M5312_HM12_Rivers-164 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H0DNF0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.5, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.72→41.09 Å / Num. obs: 200402 / % possible obs: 99.36 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.52 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.71
Reflection shellResolution: 1.72→1.782 Å / Mean I/σ(I) obs: 0.84 / Num. unique obs: 20469 / CC1/2: 0.462

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→41.09 Å / SU ML: 0.2807 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.0994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 2094 1.1 %
Rwork0.2137 188288 -
obs0.2138 190382 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.86 Å2
Refinement stepCycle: LAST / Resolution: 1.72→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 0 0 875 7035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346368
X-RAY DIFFRACTIONf_angle_d0.71718636
X-RAY DIFFRACTIONf_chiral_restr0.0507920
X-RAY DIFFRACTIONf_plane_restr0.00491108
X-RAY DIFFRACTIONf_dihedral_angle_d6.019868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.37881400.390412634X-RAY DIFFRACTION99.2
1.76-1.80.39671420.365712601X-RAY DIFFRACTION99.26
1.8-1.850.38231390.350312552X-RAY DIFFRACTION99.13
1.85-1.910.34571380.332612525X-RAY DIFFRACTION98.66
1.91-1.970.33671360.296412526X-RAY DIFFRACTION98.41
1.97-2.040.3261400.254912515X-RAY DIFFRACTION99.26
2.04-2.120.23291420.240912632X-RAY DIFFRACTION99.21
2.12-2.220.25111420.231612607X-RAY DIFFRACTION99.15
2.22-2.330.22881380.223612413X-RAY DIFFRACTION97.92
2.33-2.480.29091360.228412652X-RAY DIFFRACTION98.77
2.48-2.670.26631410.223112519X-RAY DIFFRACTION99.29
2.67-2.940.26931420.214612588X-RAY DIFFRACTION98.97
2.94-3.370.17181390.183112520X-RAY DIFFRACTION98.59
3.37-4.240.16161410.165512545X-RAY DIFFRACTION99.07
4.24-41.090.17561380.164112459X-RAY DIFFRACTION97.95

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