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- PDB-8kbb: Structure of apo-CmTad1 -

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Basic information

Entry
Database: PDB / ID: 8kbb
TitleStructure of apo-CmTad1
ComponentsThoeris anti-defense 1
KeywordsVIRAL PROTEIN
Function / homology: / Acb2/Tad1, hairpin domain / nucleotide binding / Thoeris anti-defense 1
Function and homology information
Biological speciesClostridioides mangenotii LM2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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

Downloads & links

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Assembly

Deposited unit
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
G: Thoeris anti-defense 1
H: Thoeris anti-defense 1
I: Thoeris anti-defense 1
J: Thoeris anti-defense 1
K: Thoeris anti-defense 1
L: Thoeris anti-defense 1
C: Thoeris anti-defense 1
D: Thoeris anti-defense 1
E: Thoeris anti-defense 1
F: Thoeris anti-defense 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,46314
Polymers182,33212
Non-polymers1312
Water9,998555
1
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
G: Thoeris anti-defense 1
H: Thoeris anti-defense 1
I: Thoeris anti-defense 1
J: Thoeris anti-defense 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2317
Polymers91,1666
Non-polymers651
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23890 Å2
ΔGint-222 kcal/mol
Surface area34620 Å2
MethodPISA
2
K: Thoeris anti-defense 1
L: Thoeris anti-defense 1
C: Thoeris anti-defense 1
D: Thoeris anti-defense 1
E: Thoeris anti-defense 1
F: Thoeris anti-defense 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2317
Polymers91,1666
Non-polymers651
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24140 Å2
ΔGint-219 kcal/mol
Surface area33810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.848, 144.516, 150.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thoeris anti-defense 1


Mass: 15194.333 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides mangenotii LM2 (bacteria)
Strain: LM2 / Gene: tad1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW61
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.19 Å3/Da / Density % sol: 70.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate, 1.4% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.56→42.28 Å / Num. obs: 97659 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.069 / Rrim(I) all: 0.251 / Χ2: 0.93 / Net I/σ(I): 10.1 / Num. measured all: 1255851
Reflection shellResolution: 2.56→2.63 Å / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 2.489 / Num. measured all: 91653 / Num. unique obs: 7159 / CC1/2: 0.62 / Rpim(I) all: 0.719 / Χ2: 0.8 / Net I/σ(I) obs: 1.1

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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: 2.56→41.13 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 1994 2.06 %
Rwork0.2273 --
obs0.2281 97019 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12583 0 2 555 13140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812839
X-RAY DIFFRACTIONf_angle_d1.0917285
X-RAY DIFFRACTIONf_dihedral_angle_d12.4121685
X-RAY DIFFRACTIONf_chiral_restr0.0571828
X-RAY DIFFRACTIONf_plane_restr0.0072246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.620.35231280.32926546X-RAY DIFFRACTION96
2.62-2.690.34031610.29926705X-RAY DIFFRACTION99
2.69-2.770.33341410.30036705X-RAY DIFFRACTION100
2.77-2.860.37751270.30166745X-RAY DIFFRACTION100
2.86-2.960.31571400.28776760X-RAY DIFFRACTION100
2.96-3.080.27741420.27126782X-RAY DIFFRACTION100
3.08-3.220.2431450.25366740X-RAY DIFFRACTION99
3.22-3.390.27341390.25086766X-RAY DIFFRACTION99
3.39-3.610.29361380.23246751X-RAY DIFFRACTION99
3.61-3.880.26951370.21166763X-RAY DIFFRACTION99
3.88-4.280.2331430.18846786X-RAY DIFFRACTION99
4.28-4.890.20931540.17046857X-RAY DIFFRACTION100
4.89-6.160.2631450.20016934X-RAY DIFFRACTION100
6.16-41.130.20461540.18977185X-RAY DIFFRACTION100

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