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- PDB-9b7d: Structure of ThsB-Tad3 complex -

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Basic information

Entry
Database: PDB / ID: 9b7d
TitleStructure of ThsB-Tad3 complex
Components
  • Putative cyclic ADP-D-ribose synthase ThsB1
  • Tad3
KeywordsVIRAL PROTEIN / Immune evasion / Thoeris
Function / homologyThoeris protein ThsB, TIR-like domain superfamily / Thoeris protein ThsB, TIR-like domain / Thoeris protein ThsB, TIR-like domain / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to virus / hydrolase activity / cytoplasm / Putative cyclic ADP-D-ribose synthase ThsB1
Function and homology information
Biological speciesBacillus cereus (bacteria)
metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHobbs, S.J. / Tan, J.M.J. / Yirmiya, E. / Sorek, R. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250 United States
CitationJournal: Cell / Year: 2025
Title: Structure-guided discovery of viral proteins that inhibit host immunity.
Authors: Yirmiya, E. / Hobbs, S.J. / Leavitt, A. / Osterman, I. / Avraham, C. / Hochhauser, D. / Madhala, B. / Skovorodka, M. / Tan, J.M.J. / Toyoda, H.C. / Chebotar, I. / Itkin, M. / Malitsky, S. / ...Authors: Yirmiya, E. / Hobbs, S.J. / Leavitt, A. / Osterman, I. / Avraham, C. / Hochhauser, D. / Madhala, B. / Skovorodka, M. / Tan, J.M.J. / Toyoda, H.C. / Chebotar, I. / Itkin, M. / Malitsky, S. / Amitai, G. / Kranzusch, P.J. / Sorek, R.
History
DepositionMar 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cyclic ADP-D-ribose synthase ThsB1
B: Tad3
C: Putative cyclic ADP-D-ribose synthase ThsB1
D: Tad3


Theoretical massNumber of molelcules
Total (without water)89,9954
Polymers89,9954
Non-polymers00
Water13,818767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14060 Å2
ΔGint-85 kcal/mol
Surface area34110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.937, 80.650, 72.323
Angle α, β, γ (deg.)90.000, 99.840, 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 Putative cyclic ADP-D-ribose synthase ThsB1 / Putative cADPR synthase ThsB1 / Thoeris protein ThsB


Mass: 22439.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: thsB1, thsB, II9_05449 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: J8G8J6, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Protein Tad3


Mass: 22557.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0 0.2 M MgCl2 25% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→35.63 Å / Num. obs: 75023 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.51 Å2 / CC1/2: 0.998 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 4316 / Rpim(I) all: 0.765

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.63 Å / SU ML: 0.2047 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2207 2004 2.68 %
Rwork0.1841 72906 -
obs0.1851 74910 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 0 767 6983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00376403
X-RAY DIFFRACTIONf_angle_d0.65528660
X-RAY DIFFRACTIONf_chiral_restr0.047884
X-RAY DIFFRACTIONf_plane_restr0.0051116
X-RAY DIFFRACTIONf_dihedral_angle_d5.7764835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.35351400.29045018X-RAY DIFFRACTION96.25
1.84-1.890.25141330.24745184X-RAY DIFFRACTION98.72
1.89-1.950.30831420.22925111X-RAY DIFFRACTION98.35
1.95-2.010.24411430.21815239X-RAY DIFFRACTION99.93
2.01-2.090.23311450.20975218X-RAY DIFFRACTION99.93
2.09-2.170.24431410.19325228X-RAY DIFFRACTION99.87
2.17-2.270.23821480.18655225X-RAY DIFFRACTION99.8
2.27-2.390.23311400.19025211X-RAY DIFFRACTION99.68
2.39-2.540.24881460.19545196X-RAY DIFFRACTION99.28
2.54-2.730.26611460.20145166X-RAY DIFFRACTION98.64
2.73-3.010.24941460.18925266X-RAY DIFFRACTION99.5
3.01-3.440.19571440.17915248X-RAY DIFFRACTION99.93
3.44-4.330.18311450.15015258X-RAY DIFFRACTION99.89
4.34-35.630.19181450.17035338X-RAY DIFFRACTION99.19
Refinement TLS params.Method: refined / Origin x: -17.1766205307 Å / Origin y: -11.3157477284 Å / Origin z: -45.634775791 Å
111213212223313233
T0.197063237914 Å20.000174527646958 Å20.0098385941117 Å2-0.147065133807 Å20.0117623044402 Å2--0.165768051064 Å2
L0.603131293075 °20.103171145135 °20.273789933802 °2-0.261165474626 °20.0548800417404 °2--0.391930549964 °2
S0.00573969413203 Å °-0.0215051311781 Å °-0.00455601155259 Å °0.00567923095718 Å °-0.00500570510497 Å °-0.0679321967058 Å °0.00402101614859 Å °-0.0154085762996 Å °-0.00716630080579 Å °
Refinement TLS groupSelection details: all

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