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- PDB-8kbm: Structure of AcrIIA7 complexed with cGG -

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Basic information

Entry
Database: PDB / ID: 8kbm
TitleStructure of AcrIIA7 complexed with 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 / Inhibitor of Type II CRISPR-Cas system
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 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 23, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,4144
Polymers24,0342
Non-polymers1,3812
Water4,774265
1
A: Inhibitor of Type II CRISPR-Cas system
B: Inhibitor of Type II CRISPR-Cas system
hetero molecules

A: Inhibitor of Type II CRISPR-Cas system
B: Inhibitor of Type II CRISPR-Cas system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8298
Polymers48,0674
Non-polymers2,7624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area13680 Å2
ΔGint-64 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.065, 89.846, 63.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-378-

HOH

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Components

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


Mass: 12016.822 Da / Num. of mol.: 2
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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.0 M Lithium chloride, 20% w/v Polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.38→19.77 Å / Num. obs: 97761 / % possible obs: 97.9 % / Redundancy: 26.4 % / Rrim(I) all: 0.109 / Net I/σ(I): 15
Reflection shellResolution: 1.38→1.45 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4952

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→19.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 3226 3.3 %
Rwork0.203 --
obs0.2035 97761 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 265 2001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121784
X-RAY DIFFRACTIONf_angle_d1.3982432
X-RAY DIFFRACTIONf_dihedral_angle_d17.831696
X-RAY DIFFRACTIONf_chiral_restr0.107264
X-RAY DIFFRACTIONf_plane_restr0.006294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.3931380.40574027X-RAY DIFFRACTION96
1.4-1.420.37411230.36514032X-RAY DIFFRACTION96
1.42-1.450.37921430.34574023X-RAY DIFFRACTION96
1.45-1.470.38841480.32524074X-RAY DIFFRACTION97
1.47-1.50.35461400.30594090X-RAY DIFFRACTION97
1.5-1.530.35991400.29044015X-RAY DIFFRACTION97
1.53-1.560.30021210.2814089X-RAY DIFFRACTION97
1.56-1.590.281400.27184059X-RAY DIFFRACTION97
1.59-1.630.30211340.2534076X-RAY DIFFRACTION98
1.63-1.670.30181280.25134131X-RAY DIFFRACTION98
1.67-1.710.28181530.24794126X-RAY DIFFRACTION98
1.71-1.760.25271370.23984103X-RAY DIFFRACTION98
1.76-1.820.23851550.22264115X-RAY DIFFRACTION99
1.82-1.890.24611260.21724129X-RAY DIFFRACTION99
1.89-1.960.26321540.20684141X-RAY DIFFRACTION98
1.96-2.050.22761360.19914098X-RAY DIFFRACTION99
2.05-2.160.21561510.19274193X-RAY DIFFRACTION99
2.16-2.290.21741440.18984123X-RAY DIFFRACTION99
2.29-2.470.21091450.19394189X-RAY DIFFRACTION100
2.47-2.720.20951300.19444187X-RAY DIFFRACTION100
2.72-3.110.21471280.19044161X-RAY DIFFRACTION99
3.11-3.910.16081740.17464170X-RAY DIFFRACTION100
3.92-19.770.18231380.17144184X-RAY DIFFRACTION100

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