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- PDB-8kbg: Structure of CbTad1 complexed with 2',3'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 8kbg
TitleStructure of CbTad1 complexed with 2',3'-cGAMP
ComponentsThoeris anti-defense 1
KeywordsVIRAL PROTEIN
Function / homologynucleotide binding / cGAMP / Thoeris anti-defense 1
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsXiao, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of CbTad1 complexed with 2',3'-cGAMP
Authors: Xiao, Y. / Feng, Y.
History
DepositionAug 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,51012
Polymers85,4646
Non-polymers4,0466
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27610 Å2
ΔGint-123 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.900, 66.040, 89.370
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thoeris anti-defense 1 / cbTad1


Mass: 14244.002 Da / Num. of mol.: 6
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-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MIB pH 6.0, 55% v/v 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: 2.37→35.57 Å / Num. obs: 33894 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.066 / Rrim(I) all: 0.174 / Χ2: 0.95 / Net I/σ(I): 10.2 / Num. measured all: 230965
Reflection shellResolution: 2.37→2.43 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.4 / Num. measured all: 17590 / Num. unique obs: 2488 / CC1/2: 0.552 / Rpim(I) all: 0.567 / Rrim(I) all: 1.512 / Χ2: 0.97 / Net I/σ(I) obs: 1.8

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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: 2.37→31.47 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 1630 4.81 %
Rwork0.2063 --
obs0.2083 33876 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6252 0 0 94 6346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126366
X-RAY DIFFRACTIONf_angle_d2.0288592
X-RAY DIFFRACTIONf_dihedral_angle_d19.3361080
X-RAY DIFFRACTIONf_chiral_restr0.09924
X-RAY DIFFRACTIONf_plane_restr0.0111086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.440.35971270.30692687X-RAY DIFFRACTION100
2.44-2.520.36231280.28972660X-RAY DIFFRACTION100
2.52-2.610.29241360.27562657X-RAY DIFFRACTION100
2.61-2.710.2681280.25752706X-RAY DIFFRACTION100
2.71-2.840.30651480.25842639X-RAY DIFFRACTION100
2.84-2.990.31441480.2382688X-RAY DIFFRACTION100
2.99-3.170.31541280.24172680X-RAY DIFFRACTION100
3.17-3.420.25971450.22122673X-RAY DIFFRACTION100
3.42-3.760.23321380.19932687X-RAY DIFFRACTION100
3.76-4.30.22361310.18022706X-RAY DIFFRACTION100
4.3-5.420.22571240.17162710X-RAY DIFFRACTION100
5.42-31.470.1781490.1672753X-RAY DIFFRACTION99

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