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- PDB-8kbh: Structure of CbTad1 complexed with 2',3'-cGAMP and cA3 -

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Basic information

Entry
Database: PDB / ID: 8kbh
TitleStructure of CbTad1 complexed with 2',3'-cGAMP and cA3
Components
  • (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
  • (Thoeris anti-defense 1) x 2
KeywordsVIRAL PROTEIN
Function / homology: / Acb2/Tad1, hairpin domain / nucleotide binding / cGAMP / RNA / Thoeris anti-defense 1
Function and homology information
Biological speciesClostridium botulinum (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 21, 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

Downloads & links

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Assembly

Deposited unit
D: Thoeris anti-defense 1
E: Thoeris anti-defense 1
F: Thoeris anti-defense 1
G: Thoeris anti-defense 1
H: Thoeris anti-defense 1
I: Thoeris anti-defense 1
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
C: Thoeris anti-defense 1
J: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
K: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
L: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,73921
Polymers131,67012
Non-polymers6,0709
Water28,8241600
1
D: Thoeris anti-defense 1
E: Thoeris anti-defense 1
F: Thoeris anti-defense 1
G: Thoeris anti-defense 1
H: Thoeris anti-defense 1
I: Thoeris anti-defense 1
J: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
K: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,75014
Polymers87,7048
Non-polymers4,0466
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29570 Å2
ΔGint-130 kcal/mol
Surface area30210 Å2
MethodPISA
2
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
C: Thoeris anti-defense 1
L: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
hetero molecules

A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
C: Thoeris anti-defense 1
L: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,97814
Polymers87,9328
Non-polymers4,0466
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area29560 Å2
ΔGint-129 kcal/mol
Surface area31530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.725, 81.244, 128.586
Angle α, β, γ (deg.)90.00, 106.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-651-

HOH

21C-507-

HOH

31C-658-

HOH

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Components

#1: Protein
Thoeris anti-defense 1 / cbTad1


Mass: 14341.115 Da / Num. of mol.: 8
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: Protein Thoeris anti-defense 1 / cbTad1


Mass: 14112.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: tad1, ACP51_06460 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW58
#3: RNA chain (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE


Mass: 942.660 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1600 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M PCTP pH 8.0, 60% MPD

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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 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.54→35.13 Å / Num. obs: 205128 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.965 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.089 / Rrim(I) all: 0.218 / Χ2: 0.81 / Net I/σ(I): 5.8 / Num. measured all: 1251059
Reflection shellResolution: 1.54→1.58 Å / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 1.14 / Num. measured all: 72068 / Num. unique obs: 15133 / CC1/2: 0.28 / Rpim(I) all: 0.591 / Χ2: 0.58 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→35.12 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 10159 4.96 %
Rwork0.2308 --
obs0.2323 204902 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9589 0 0 1600 11189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089790
X-RAY DIFFRACTIONf_angle_d1.24513262
X-RAY DIFFRACTIONf_dihedral_angle_d22.7121721
X-RAY DIFFRACTIONf_chiral_restr0.0681424
X-RAY DIFFRACTIONf_plane_restr0.0071640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.33383310.29976149X-RAY DIFFRACTION95
1.56-1.580.31413690.30466415X-RAY DIFFRACTION100
1.58-1.590.32533130.30066535X-RAY DIFFRACTION100
1.59-1.610.28812960.27776477X-RAY DIFFRACTION100
1.61-1.640.29513410.276470X-RAY DIFFRACTION100
1.64-1.660.30793360.25866524X-RAY DIFFRACTION100
1.66-1.680.30263050.25796438X-RAY DIFFRACTION100
1.68-1.710.28623500.24856468X-RAY DIFFRACTION100
1.71-1.730.26713510.24126529X-RAY DIFFRACTION100
1.73-1.760.2993390.26346481X-RAY DIFFRACTION100
1.76-1.790.31633360.26746418X-RAY DIFFRACTION100
1.79-1.830.32472930.29336533X-RAY DIFFRACTION100
1.83-1.860.28913260.25656485X-RAY DIFFRACTION100
1.86-1.90.29073700.2526473X-RAY DIFFRACTION100
1.9-1.940.28043530.24656486X-RAY DIFFRACTION100
1.94-1.980.28163530.23846479X-RAY DIFFRACTION100
1.98-2.030.26553160.24526539X-RAY DIFFRACTION100
2.03-2.090.2943160.23336445X-RAY DIFFRACTION100
2.09-2.150.2573260.22126506X-RAY DIFFRACTION100
2.15-2.220.2463430.21976469X-RAY DIFFRACTION100
2.22-2.30.26223210.22896563X-RAY DIFFRACTION100
2.3-2.390.263420.22476541X-RAY DIFFRACTION100
2.39-2.50.24533350.22676479X-RAY DIFFRACTION100
2.5-2.630.26063450.22586517X-RAY DIFFRACTION100
2.63-2.80.24743390.21666546X-RAY DIFFRACTION100
2.8-3.010.24533560.2196484X-RAY DIFFRACTION100
3.01-3.320.25363490.20716512X-RAY DIFFRACTION100
3.32-3.790.21083820.18616526X-RAY DIFFRACTION100
3.79-4.780.19253530.17836604X-RAY DIFFRACTION100
4.78-35.120.23923740.21946652X-RAY DIFFRACTION100

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