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- PDB-7t26: Structure of phage FBB1 anti-CBASS nuclease Acb1 in apo state -

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Basic information

Entry
Database: PDB / ID: 7t26
TitleStructure of phage FBB1 anti-CBASS nuclease Acb1 in apo state
ComponentsAcb1
KeywordsVIRAL PROTEIN / Anti-CBASS / Nuclease / Immune evasion
Function / homologyCyclic phosphodiesterase / hydrolase activity / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / Anti-CBASS protein Acb1
Function and homology information
Biological speciesErwinia phage FBB1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.14 Å
AuthorsHobbs, S.J. / Wein, T. / Lu, A. / Morehouse, B.R. / Schnabel, J. / Sorek, R. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Nature / Year: 2022
Title: Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity.
Authors: Hobbs, S.J. / Wein, T. / Lu, A. / Morehouse, B.R. / Schnabel, J. / Leavitt, A. / Yirmiya, E. / Sorek, R. / Kranzusch, P.J.
History
DepositionDec 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acb1


Theoretical massNumber of molelcules
Total (without water)16,2651
Polymers16,2651
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.845, 43.845, 154.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Acb1


Mass: 16265.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia phage FBB1 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A868BQY3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2 M Ammonium Sulfate, 0.1 M Sodium Citrate pH 4.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.14→43.19 Å / Num. obs: 53419 / % possible obs: 99.5 % / Redundancy: 24 % / Biso Wilson estimate: 14.43 Å2 / CC1/2: 1 / Rpim(I) all: 0.012 / Net I/σ(I): 23.3
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2479 / CC1/2: 0.844 / Rpim(I) all: 0.377 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.14→42.17 Å / SU ML: 0.0886 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7989
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1808 2231 4.19 %
Rwork0.1602 51015 -
obs0.161 53246 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.35 Å2
Refinement stepCycle: LAST / Resolution: 1.14→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 0 246 1332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01081133
X-RAY DIFFRACTIONf_angle_d1.28051547
X-RAY DIFFRACTIONf_chiral_restr0.0828175
X-RAY DIFFRACTIONf_plane_restr0.0115199
X-RAY DIFFRACTIONf_dihedral_angle_d12.0542427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.170.2162460.18291038X-RAY DIFFRACTION31.7
1.17-1.190.27241410.21873221X-RAY DIFFRACTION97.65
1.19-1.220.22141400.19223218X-RAY DIFFRACTION98.45
1.22-1.260.20191420.16783259X-RAY DIFFRACTION99.5
1.26-1.290.18751450.16383290X-RAY DIFFRACTION99.77
1.29-1.340.19931420.15653252X-RAY DIFFRACTION99.88
1.34-1.380.18241430.16163300X-RAY DIFFRACTION99.8
1.38-1.440.1861430.1653287X-RAY DIFFRACTION99.74
1.44-1.50.20331460.16183307X-RAY DIFFRACTION99.77
1.5-1.580.19781450.14593316X-RAY DIFFRACTION99.94
1.58-1.680.17431460.13763332X-RAY DIFFRACTION99.74
1.68-1.810.17731450.14263335X-RAY DIFFRACTION99.91
1.81-20.16071480.14113372X-RAY DIFFRACTION99.97
2-2.280.14921480.13473384X-RAY DIFFRACTION100
2.28-2.880.17511500.16153440X-RAY DIFFRACTION100
2.88-42.170.19041610.17783664X-RAY DIFFRACTION99.92

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