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- PDB-8kbk: Structure of AcrIIA7 complexed with 1',2'-cADPR and cGG -

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Basic information

Entry
Database: PDB / ID: 8kbk
TitleStructure of AcrIIA7 complexed with 1',2'-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-MF6 / Inhibitor of Type II CRISPR-Cas system
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 6, 2024Group: Database references / Category: citation / citation_author
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
Revision 1.3Nov 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 1.4Dec 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: Inhibitor of Type II CRISPR-Cas system
D: Inhibitor of Type II CRISPR-Cas system
B: Inhibitor of Type II CRISPR-Cas system
C: Inhibitor of Type II CRISPR-Cas system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5318
Polymers48,0674
Non-polymers2,4634
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-68 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.270, 57.690, 92.510
Angle α, β, γ (deg.)90.00, 121.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Inhibitor of Type II CRISPR-Cas system / AcrIIA7


Mass: 12016.822 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-MF6 / (1S,3R,4R,6R,9S,11R,14R,15S,16R,18R)-4-(6-amino-9H-purin-9-yl)-9,11,15,16,18-pentahydroxy-2,5,8,10,12,17-hexaoxa-9lambda~5~,11lambda~5~-diphosphatricyclo[12.2.1.1~3,6~]octadecane-9,11-dione / 1'-2' gcADPR


Mass: 541.300 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium thiocyanate, 20% w/v Polyethylene glycol 3350

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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 S 9M / 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: 2.28→47.76 Å / Num. obs: 21073 / % possible obs: 98.2 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 1 / Net I/σ(I): 11.5 / Num. measured all: 143086
Reflection shellResolution: 2.28→2.34 Å / % possible obs: 97.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 1.211 / Num. measured all: 9675 / Num. unique obs: 1528 / CC1/2: 0.73 / Rpim(I) all: 0.523 / Χ2: 0.96 / Net I/σ(I) obs: 1.7

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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: 2.28→27.08 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 1080 5.13 %
Rwork0.2288 --
obs0.2319 21044 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 46 31 3461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113600
X-RAY DIFFRACTIONf_angle_d2.0564916
X-RAY DIFFRACTIONf_dihedral_angle_d23.522604
X-RAY DIFFRACTIONf_chiral_restr0.122538
X-RAY DIFFRACTIONf_plane_restr0.013582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.380.39651180.32982480X-RAY DIFFRACTION97
2.38-2.510.3951430.31892447X-RAY DIFFRACTION97
2.51-2.670.39971280.30172454X-RAY DIFFRACTION97
2.67-2.870.40091330.29192499X-RAY DIFFRACTION98
2.87-3.160.32531170.2792518X-RAY DIFFRACTION98
3.16-3.620.30361680.23842473X-RAY DIFFRACTION98
3.62-4.550.24431380.19272523X-RAY DIFFRACTION99
4.55-27.080.24161350.1942570X-RAY DIFFRACTION98

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