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- PDB-8wjd: Structure of SptTad2 complexed with cGG -

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Basic information

Entry
Database: PDB / ID: 8wjd
TitleStructure of SptTad2 complexed with cGG
ComponentsSptTad2
KeywordsVIRAL PROTEIN
Function / homologyChem-C2E
Function and homology information
Biological speciesSphingobacterium thalpophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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
DepositionSep 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 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:
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Assembly

Deposited unit
A: SptTad2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2892
Polymers11,5981
Non-polymers6901
Water79344
1
A: SptTad2
hetero molecules

A: SptTad2
hetero molecules

A: SptTad2
hetero molecules

A: SptTad2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1548
Polymers46,3934
Non-polymers2,7624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area13640 Å2
ΔGint-37 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.550, 61.550, 97.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein SptTad2


Mass: 11598.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium thalpophilum (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Magnesium nitrate hexahydrate, Tris pH8.0, PEG2000

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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: Sep 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.71→48.76 Å / Num. obs: 12316 / % possible obs: 99.2 % / Redundancy: 35.3 % / Rrim(I) all: 0.093 / Net I/σ(I): 25.8
Reflection shellResolution: 1.71→1.75 Å / Num. unique obs: 881

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→32.5 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 600 4.89 %
Rwork0.2106 --
obs0.212 12277 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 46 44 906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011887
X-RAY DIFFRACTIONf_angle_d1.3721205
X-RAY DIFFRACTIONf_dihedral_angle_d19.499150
X-RAY DIFFRACTIONf_chiral_restr0.094123
X-RAY DIFFRACTIONf_plane_restr0.007150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.880.31981440.28772843X-RAY DIFFRACTION100
1.88-2.150.27391420.27062817X-RAY DIFFRACTION97
2.15-2.710.29231400.252916X-RAY DIFFRACTION99
2.71-32.50.21261740.18473101X-RAY DIFFRACTION100

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