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- PDB-8gbe: Structure of a viral gasdermin protein A47 from Eptesipox virus -

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Basic information

Entry
Database: PDB / ID: 8gbe
TitleStructure of a viral gasdermin protein A47 from Eptesipox virus
ComponentsProtein A47
KeywordsVIRAL PROTEIN / viral mimicry / gasdermin / caspase / autoinhibition / pyroptosis / bats / immunity / cell death / immune system
Function / homologyGasdermin / Orthopoxvirus A47 / Orthopoxvirus A47 protein / Gasdermin, PUB domain / Gasdermin PUB domain / Protein A47
Function and homology information
Biological speciesEptesipox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.46 Å
AuthorsJohnson, A.G. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biorxiv / Year: 2023
Title: Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses.
Authors: Boys, I.N. / Johnson, A.G. / Quinlan, M. / Kranzusch, P.J. / Elde, N.C.
History
DepositionFeb 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein A47


Theoretical massNumber of molelcules
Total (without water)23,8031
Polymers23,8031
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.465, 74.140, 95.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

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Components

#1: Protein Protein A47


Mass: 23802.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eptesipox virus / Gene: EPTV-WA-146 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: A0A220T6L2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 100 mM ADA and 40% PEG-200

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.46→48.65 Å / Num. obs: 40114 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 21.91 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/σ(I): 18.3
Reflection shellResolution: 1.46→1.48 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1969 / CC1/2: 0.505 / Rpim(I) all: 0.718 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.46→48.65 Å / SU ML: 0.1496 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 2000 5 %
Rwork0.1905 38033 -
obs0.1915 40033 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.31 Å2
Refinement stepCycle: LAST / Resolution: 1.46→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 0 85 1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121688
X-RAY DIFFRACTIONf_angle_d1.09592289
X-RAY DIFFRACTIONf_chiral_restr0.0831281
X-RAY DIFFRACTIONf_plane_restr0.0066279
X-RAY DIFFRACTIONf_dihedral_angle_d16.4622627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.26041390.26172652X-RAY DIFFRACTION98.03
1.5-1.540.25991420.23452685X-RAY DIFFRACTION100
1.54-1.580.24831400.21572682X-RAY DIFFRACTION100
1.58-1.630.23981420.21222688X-RAY DIFFRACTION100
1.63-1.690.21981420.20492699X-RAY DIFFRACTION99.96
1.69-1.760.23391410.20112693X-RAY DIFFRACTION100
1.76-1.840.25481430.20662691X-RAY DIFFRACTION100
1.84-1.940.21091410.18662697X-RAY DIFFRACTION99.96
1.94-2.060.21421430.17352717X-RAY DIFFRACTION100
2.06-2.220.17591420.16892719X-RAY DIFFRACTION99.93
2.22-2.440.20221440.1692724X-RAY DIFFRACTION100
2.44-2.790.1731440.17792737X-RAY DIFFRACTION100
2.79-3.520.22521460.18372778X-RAY DIFFRACTION99.97
3.52-48.650.2151510.20272871X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.272082102050.358725166091.139146685740.78459575989-0.6346429247952.03235349780.0975828249037-0.106803203441-0.1946858956170.139442181298-0.17895934359-0.2093574014290.1374670221840.4644361987720.004307289818840.206170382360.00239828257557-0.02369786752080.106707974540.03506586782290.25423552203114.280139045842.411921902331.1895323009
20.752723677268-0.8142244993150.1489711891811.379413836040.4206533823880.7677351980990.1866434896940.12604572698-0.0520255782829-0.136665797684-0.1464722264730.02279138407430.05180685126490.1122567672880.009095910885520.196826451620.0419389898586-0.01717072347810.210718949077-0.002629579937260.1900912257987.060346364539.294533274415.4224564205
31.638653603850.6709635165440.4234864148572.08219509010.01645265790781.7459435280.0461355417802-0.0304430666637-0.06752868336930.0912845697158-0.0697289679341-0.214850160426-0.2217132757510.184251394826-0.002568289413750.202207292499-0.0601683585876-0.04131804234840.1918506257590.02085613988630.21793473070215.609156489953.948115316436.0585885772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 217 )

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