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- PDB-8kbe: Structure of CbTad1 complexed with 1',3'-cADPR -

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Basic information

Entry
Database: PDB / ID: 8kbe
TitleStructure of CbTad1 complexed with 1',3'-cADPR
ComponentsThoeris anti-defense 1
KeywordsVIRAL PROTEIN
Function / homology: / Acb2/Tad1, hairpin domain / nucleotide binding / Chem-OJC / Thoeris anti-defense 1
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsXiao, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2024
Title: Single phage proteins sequester signals from TIR and cGAS-like enzymes.
Authors: Li, D. / Xiao, Y. / Fedorova, I. / Xiong, W. / Wang, Y. / Liu, X. / Huiting, E. / Ren, J. / Gao, Z. / Zhao, X. / Cao, X. / Zhang, Y. / Bondy-Denomy, J. / Feng, Y.
History
DepositionAug 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 4, 2024Group: Data collection / Database references / Category: citation / citation_author / reflns_shell
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _reflns_shell.pdbx_Rrim_I_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8084
Polymers31,7252
Non-polymers1,0832
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-38 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.090, 101.090, 101.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Thoeris anti-defense 1


Mass: 15862.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: tad1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW58
#2: Chemical ChemComp-OJC / (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione


Mass: 541.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 3.2 M Ammonium sulfate, 0.1 M Citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.16→35.74 Å / Num. obs: 18785 / % possible obs: 100 % / Redundancy: 35.1 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.012 / Rrim(I) all: 0.071 / Χ2: 0.95 / Net I/σ(I): 31.3 / Num. measured all: 660157
Reflection shellResolution: 2.16→2.22 Å / % possible obs: 100 % / Redundancy: 17.8 % / Rmerge(I) obs: 1.232 / Num. measured all: 24972 / Num. unique obs: 1399 / CC1/2: 0.791 / Rpim(I) all: 0.293 / Χ2: 0.83 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7uaw

7uaw


Resolution: 2.16→31.97 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 941 5.02 %
Rwork0.2051 --
obs0.2071 18756 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 70 45 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062168
X-RAY DIFFRACTIONf_angle_d1.2752921
X-RAY DIFFRACTIONf_dihedral_angle_d15.428422
X-RAY DIFFRACTIONf_chiral_restr0.062315
X-RAY DIFFRACTIONf_plane_restr0.005373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.270.32121300.26962516X-RAY DIFFRACTION100
2.27-2.420.28531560.23062475X-RAY DIFFRACTION100
2.42-2.60.32021440.27832537X-RAY DIFFRACTION100
2.6-2.860.30161300.27262517X-RAY DIFFRACTION100
2.86-3.280.28881250.23842539X-RAY DIFFRACTION100
3.28-4.130.21591270.19662574X-RAY DIFFRACTION100
4.13-31.970.22771290.16772657X-RAY DIFFRACTION100

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