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- PDB-8wjc: Structure of AcrIIA7 complexed with 3'3'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 8wjc
TitleStructure of AcrIIA7 complexed with 3'3'-cGAMP
ComponentsInhibitor of Type II CRISPR-Cas system
KeywordsVIRAL PROTEIN
Function / homologyProtein of unknown function DUF2829 / Thoeris anti-defense 2-like domain / nucleotide binding / Chem-4BW / Inhibitor of Type II CRISPR-Cas system
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inhibitor of Type II CRISPR-Cas system
B: Inhibitor of Type II CRISPR-Cas system
C: Inhibitor of Type II CRISPR-Cas system
D: Inhibitor of Type II CRISPR-Cas system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2916
Polymers46,9424
Non-polymers1,3492
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-72 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.200, 81.550, 50.380
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11735.451 Da / Num. of mol.: 4
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-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Magnesium nitrate hexahydrate, HEPES pH 7.5, Poly (acrylic acid sodium salt) 5100

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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 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.11→31.4 Å / Num. obs: 22837 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rrim(I) all: 0.215 / Net I/σ(I): 8.5
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 6.5 % / Num. unique obs: 1672

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→31.4 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2737 1160 5.09 %
Rwork0.2237 --
obs0.2263 22795 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 45 73 3451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013462
X-RAY DIFFRACTIONf_angle_d1.3144696
X-RAY DIFFRACTIONf_dihedral_angle_d12.176484
X-RAY DIFFRACTIONf_chiral_restr0.161504
X-RAY DIFFRACTIONf_plane_restr0.006584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.210.32291390.29332682X-RAY DIFFRACTION100
2.21-2.320.40261460.32062684X-RAY DIFFRACTION99
2.32-2.470.30461680.27892674X-RAY DIFFRACTION100
2.47-2.660.33851580.2672694X-RAY DIFFRACTION100
2.66-2.930.29641300.24682700X-RAY DIFFRACTION100
2.93-3.350.32511390.23312730X-RAY DIFFRACTION100
3.35-4.220.24641150.1952742X-RAY DIFFRACTION100
4.22-31.40.21841650.18822729X-RAY DIFFRACTION99

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