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- PDB-7t27: Structure of phage FBB1 anti-CBASS nuclease Acb1-3'3'-cGAMP compl... -

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Basic information

Entry
Database: PDB / ID: 7t27
TitleStructure of phage FBB1 anti-CBASS nuclease Acb1-3'3'-cGAMP complex in post reaction state
ComponentsAcb1
KeywordsVIRAL PROTEIN / Anti-CBASS / Nuclease / Immune evasion
Function / homologyCyclic phosphodiesterase / Chem-ECI / Anti-CBASS protein Acb1
Function and homology information
Biological speciesErwinia phage FBB1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 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

Downloads & links

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Assembly

Deposited unit
A: Acb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0863
Polymers16,2651
Non-polymers8212
Water3,963220
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: Chemical ChemComp-ECI / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-2-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]oxy-sulfanyl-phosphoryl]oxymethyl]-4-oxidanyl-oxolan-3-yl]oxy-sulfanyl-phosphinic acid


Mass: 724.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N10O12P2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.2→43.85 Å / Num. obs: 47842 / % possible obs: 99.1 % / Redundancy: 16.9 % / Biso Wilson estimate: 9.31 Å2 / CC1/2: 1 / Rpim(I) all: 0.013 / Net I/σ(I): 23.2
Reflection shellResolution: 1.2→1.22 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2307 / CC1/2: 0.846 / Rpim(I) all: 0.438 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→42.17 Å / SU ML: 0.1195 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.2934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1972 2000 4.19 %
Rwork0.1759 45729 -
obs0.1768 47729 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.6 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 51 220 1392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02241219
X-RAY DIFFRACTIONf_angle_d2.13751672
X-RAY DIFFRACTIONf_chiral_restr0.8447187
X-RAY DIFFRACTIONf_plane_restr0.0137205
X-RAY DIFFRACTIONf_dihedral_angle_d13.2984438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.27781330.30233036X-RAY DIFFRACTION94.01
1.23-1.260.29031370.25583141X-RAY DIFFRACTION96.64
1.26-1.30.27021370.23573150X-RAY DIFFRACTION97.8
1.3-1.340.25791420.20953210X-RAY DIFFRACTION98.36
1.34-1.390.2191400.20653201X-RAY DIFFRACTION98.99
1.39-1.450.22851410.19743232X-RAY DIFFRACTION99.29
1.45-1.510.20281430.18633284X-RAY DIFFRACTION99.39
1.51-1.590.20491410.16943215X-RAY DIFFRACTION99.64
1.59-1.690.19281440.15923301X-RAY DIFFRACTION99.86
1.69-1.820.16621450.16323302X-RAY DIFFRACTION99.97
1.82-2.010.18081450.15333304X-RAY DIFFRACTION100
2.01-2.30.16961460.14623347X-RAY DIFFRACTION100
2.3-2.890.20721470.16323387X-RAY DIFFRACTION100
2.89-42.170.1731590.17013619X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.559413448271.295544334790.846185634924.271070852383.929742717883.75137305670.0446079398298-0.0243601938881-0.08199340440410.1429124501890.0729354391506-0.07015825091240.3285974279860.323909609217-0.2000991877120.1011582054860.01727323193720.004532743001480.0465425062235-0.001274947903720.05888115499613.6751111468316.235483332680.5977586494
24.829302180761.27507050993-0.2241856558391.47003320305-0.7775595987371.4226251366-0.1922621677140.423999362549-0.119403129258-0.1759942972460.179738820829-0.1758999005330.4964017440760.2457621988360.002871226449530.09931568339360.0379561413977-0.003125059340450.101637146633-0.03325503711310.06649982770599.1218643165216.019156762162.5698212377
30.4195283006560.00213783023506-0.5895531117870.333169572131-0.2114490054921.932514260910.007906103416890.00455253523556-0.04951637569760.004740099120030.0003169709448560.002888277166170.2425840678330.099784154072-0.008506964294120.0746671014020.00690776605602-0.001208718803630.0236296032263-0.01081278099240.06081096796450.65651111750517.40741800179.6773942482
41.10713375540.835245004411-0.7980014751291.18026628679-0.3735465366221.447794637030.05806892512830.02400203384860.06949418214120.0700809269119-0.004120925475650.00542783319077-0.01675136610610.0173110625759-0.01554750444070.05295047393550.00271101128121-0.01323607126730.0565482922025-0.01245726788270.07487861456066.352908995428.212274014269.6701038851
50.4576604681040.293831900952-0.6510331945790.475780581068-0.6537643486481.334247023870.04437174382589.36439483458E-60.04097799640560.0896455172630.0316455807794-0.000397198426059-0.09438227209490.0423319299584-0.06151337009510.06350371780090.00233648653269-0.004640887737680.0473273302648-0.007291148543950.07348784575091.2251971567724.962163016574.0797735955
60.679380396917-0.840086019621-0.5668756448341.38014210392-0.03348945984163.73197833559-0.0774967981141-0.068411980432-0.0935791784593-0.2291647017530.0834678439419-0.413222295042-0.004665390321240.712763615608-0.03427517569810.1966118755210.02010740172390.02556564471310.116323446175-0.01668235267770.1459690296497.8363648479216.267528616281.75251234
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 10 )1 - 101 - 10
22chain 'A' and (resid 11 through 31 )11 - 3111 - 31
33chain 'A' and (resid 32 through 59 )32 - 5932 - 57
44chain 'A' and (resid 60 through 81 )60 - 8158 - 79
55chain 'A' and (resid 82 through 127 )82 - 12780 - 125
66chain 'A' and (resid 128 through 142 )128 - 142126 - 140

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