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- PDB-8kbl: Structure of AcrIIA7 complexed with 1',3'-cADPR and cGG -

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Basic information

Entry
Database: PDB / ID: 8kbl
TitleStructure of AcrIIA7 complexed with 1',3'-cADPR and cGG
ComponentsInhibitor of Type II CRISPR-Cas system
KeywordsVIRAL PROTEIN
Function / homologyProtein of unknown function DUF2829 / Thoeris anti-defense 2-like domain / nucleotide binding / Chem-C2E / Chem-OJC / Inhibitor of Type II CRISPR-Cas system
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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: Inhibitor of Type II CRISPR-Cas system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9673
Polymers11,7351
Non-polymers1,2322
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.729, 63.729, 63.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-201-

OJC

21A-346-

HOH

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Components

#1: Protein Inhibitor of Type II CRISPR-Cas system


Mass: 11735.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Gene: acrIIA7 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A447EB45
#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.: 1 / Source method: obtained synthetically / Formula: C15H21N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 25% w/v Polyethylene glycol 4000

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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: May 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→36.71 Å / Num. obs: 9583 / % possible obs: 100 % / Redundancy: 24.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.044 / Rrim(I) all: 0.216 / Χ2: 0.97 / Net I/σ(I): 18.6 / Num. measured all: 232505
Reflection shellResolution: 1.98→2.03 Å / % possible obs: 100 % / Redundancy: 26 % / Rmerge(I) obs: 2.161 / Num. measured all: 18088 / Num. unique obs: 697 / CC1/2: 0.983 / Rpim(I) all: 0.427 / Χ2: 0.81 / Net I/σ(I) obs: 8.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→36.68 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 430 4.49 %
Rwork0.2194 --
obs0.22 9568 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→36.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 81 89 992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016931
X-RAY DIFFRACTIONf_angle_d1.5961277
X-RAY DIFFRACTIONf_dihedral_angle_d17.601369
X-RAY DIFFRACTIONf_chiral_restr0.127140
X-RAY DIFFRACTIONf_plane_restr0.01148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.050.3314340.2588904X-RAY DIFFRACTION100
2.05-2.130.2989410.2422887X-RAY DIFFRACTION100
2.13-2.230.2463520.2349872X-RAY DIFFRACTION100
2.23-2.350.3019440.248899X-RAY DIFFRACTION100
2.35-2.490.2651430.2453895X-RAY DIFFRACTION100
2.49-2.690.2342620.244888X-RAY DIFFRACTION100
2.69-2.960.2332370.2427905X-RAY DIFFRACTION100
2.96-3.380.1957420.2174920X-RAY DIFFRACTION100
3.38-4.260.1888290.1854957X-RAY DIFFRACTION100
4.27-36.680.2258460.20021011X-RAY DIFFRACTION100

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