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- PDB-9sa5: Inhibition by ATP regulates the activity of a CBASS antiphage nuc... -

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Basic information

Entry
Database: PDB / ID: 9sa5
TitleInhibition by ATP regulates the activity of a CBASS antiphage nucleotide cyclase
ComponentsCD-NTase
KeywordsANTIVIRAL PROTEIN / CRISPR CBASS Anti-viral immune anti-phage
Function / homologyADENOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 7, 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)158,54617
Polymers153,5334
Non-polymers5,01313
Water4,234235
1
A: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7755
Polymers38,3831
Non-polymers1,3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7755
Polymers38,3831
Non-polymers1,3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2202
Polymers38,3831
Non-polymers8361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7755
Polymers38,3831
Non-polymers1,3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.296, 116.702, 156.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: obtained synthetically / Formula: C20H28N10O19P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4 M Sodium malonate dibasic monohydrate pH 7.0

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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: 2.09→78.34 Å / Num. obs: 91646 / % possible obs: 96 % / Redundancy: 5.6 % / Biso Wilson estimate: 46.64 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.1
Reflection shellResolution: 2.09→2.12 Å / Num. unique obs: 3347 / CC1/2: 0.188

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→76.25 Å / SU ML: 0.4265 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.1382
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2773 1924 2.17 %
Rwork0.2181 86819 -
obs0.2194 88743 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.4 Å2
Refinement stepCycle: LAST / Resolution: 2.09→76.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9743 0 290 235 10268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009110286
X-RAY DIFFRACTIONf_angle_d1.093113968
X-RAY DIFFRACTIONf_chiral_restr0.06261524
X-RAY DIFFRACTIONf_plane_restr0.01011734
X-RAY DIFFRACTIONf_dihedral_angle_d16.57181482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.458630.42533168X-RAY DIFFRACTION47.97
2.14-2.20.41521140.40164760X-RAY DIFFRACTION72.27
2.2-2.260.43111160.3985663X-RAY DIFFRACTION86.09
2.26-2.340.38191260.32396301X-RAY DIFFRACTION95.3
2.34-2.420.37471570.3016583X-RAY DIFFRACTION99.29
2.42-2.520.40561490.29836600X-RAY DIFFRACTION99.9
2.52-2.630.38571380.27736613X-RAY DIFFRACTION99.97
2.63-2.770.32241520.25866610X-RAY DIFFRACTION99.99
2.77-2.940.31781620.25866656X-RAY DIFFRACTION99.99
2.94-3.170.31941430.26476659X-RAY DIFFRACTION99.97
3.17-3.490.30331400.22676708X-RAY DIFFRACTION99.99
3.49-3.990.27821460.18726705X-RAY DIFFRACTION99.99
3.99-5.030.21351570.15286775X-RAY DIFFRACTION99.99
5.03-76.250.19071610.16877018X-RAY DIFFRACTION99.92

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