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- PDB-9sax: Inhibition by ATP regulates the activity of a CBASS antiphage nuc... -

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Basic information

Entry
Database: PDB / ID: 9sax
TitleInhibition by ATP regulates the activity of a CBASS antiphage nucleotide cyclase
ComponentsCD-NTase
KeywordsANTIVIRAL PROTEIN / CRISPR CBASS anti-viral anti-phage immune
Function / homology: / PHOSPHATE ION
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsMcMahon, S.A. / Gaskell-Mew, L. / Wotherspoon, P. / McQuarrie, S. / Graham, S. / Gloster, T.M. / White, M.F.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101018608European Union
CitationJournal: Biochem.J. / Year: 2026
Title: Inhibition by ATP regulates the activity of a CBASS anti-phage nucleotide cyclase.
Authors: Gaskell-Mew, L. / McQuarrie, S. / McMahon, S.A. / Wotherspoon, P. / Graham, S. / Gloster, T.M. / White, M.F.
History
DepositionAug 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD-NTase
B: CD-NTase
C: CD-NTase
D: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,25912
Polymers153,5334
Non-polymers3,7258
Water37821
1
A: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3153
Polymers38,3831
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3153
Polymers38,3831
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3153
Polymers38,3831
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3153
Polymers38,3831
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.919, 117.042, 155.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
CD-NTase


Mass: 38383.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-LQ1 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 836.387 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C20H28N10O19P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3000 0.1M Sodium citrate/ Citric acid pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.83→74.003 Å / Num. obs: 24687 / % possible obs: 91.1 % / Redundancy: 6.5 % / CC1/2: 0.998 / Net I/σ(I): 9.8
Reflection shellResolution: 2.83→3.12 Å / Num. unique obs: 1234 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→73.89 Å / SU ML: 0.3124 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.5571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2415 1206 4.89 %
Rwork0.2202 23475 -
obs0.2212 24681 66.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.37 Å2
Refinement stepCycle: LAST / Resolution: 2.83→73.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9208 0 232 21 9461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00779684
X-RAY DIFFRACTIONf_angle_d1.298913249
X-RAY DIFFRACTIONf_chiral_restr0.06951487
X-RAY DIFFRACTIONf_plane_restr0.01411681
X-RAY DIFFRACTIONf_dihedral_angle_d15.84343491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.940.182450.3478164X-RAY DIFFRACTION4.17
2.94-3.080.3534370.324601X-RAY DIFFRACTION15.62
3.08-3.240.31871030.33161720X-RAY DIFFRACTION44.63
3.24-3.440.3579970.32392195X-RAY DIFFRACTION55.97
3.44-3.710.36721540.27932909X-RAY DIFFRACTION74.42
3.71-4.080.24741990.23973782X-RAY DIFFRACTION96.25
4.08-4.670.25381990.19533961X-RAY DIFFRACTION100
4.67-5.890.23232010.20313987X-RAY DIFFRACTION100
5.89-73.890.1912110.19774156X-RAY DIFFRACTION99.82

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