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- PDB-9sa4: Inhibition by ATP regulates the activity of a CBASS antiphage nuc... -

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Basic information

Entry
Database: PDB / ID: 9sa4
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: 2.23 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)158,74827
Polymers153,5374
Non-polymers5,21123
Water3,819212
1
A: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6156
Polymers38,3841
Non-polymers1,2315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7117
Polymers38,3841
Non-polymers1,3276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7117
Polymers38,3841
Non-polymers1,3276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7117
Polymers38,3841
Non-polymers1,3276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.795, 115.601, 156.463
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: 38384.262 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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M BisTris pH5.5 1.6M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.12→100 Å / Num. obs: 90060 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 58.17 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.3
Reflection shellResolution: 2.12→2.15 Å / Num. unique obs: 4369 / CC1/2: 0.323

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→78.23 Å / SU ML: 0.4264 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3389
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2559 3834 5.01 %
Rwork0.2045 72755 -
obs0.2071 76589 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.33 Å2
Refinement stepCycle: LAST / Resolution: 2.23→78.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9670 0 307 212 10189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007710209
X-RAY DIFFRACTIONf_angle_d0.980113865
X-RAY DIFFRACTIONf_chiral_restr0.06141503
X-RAY DIFFRACTIONf_plane_restr0.00811719
X-RAY DIFFRACTIONf_dihedral_angle_d15.16971578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.260.40861040.39132257X-RAY DIFFRACTION83.72
2.26-2.290.40231320.36882560X-RAY DIFFRACTION94.39
2.29-2.320.35141560.35212584X-RAY DIFFRACTION97.89
2.32-2.350.38721400.34482654X-RAY DIFFRACTION98.14
2.35-2.390.32411200.32992668X-RAY DIFFRACTION99.29
2.39-2.420.32211390.32562712X-RAY DIFFRACTION99.93
2.42-2.460.34231530.31762662X-RAY DIFFRACTION99.89
2.46-2.510.37911360.30482701X-RAY DIFFRACTION99.89
2.51-2.550.38451330.31692710X-RAY DIFFRACTION99.96
2.55-2.60.4041530.37262675X-RAY DIFFRACTION99.96
2.6-2.650.36331490.31452697X-RAY DIFFRACTION99.93
2.65-2.710.34011490.29292710X-RAY DIFFRACTION99.86
2.71-2.780.31221240.26672689X-RAY DIFFRACTION99.96
2.78-2.850.33981450.25032708X-RAY DIFFRACTION99.89
2.85-2.920.2881340.23992710X-RAY DIFFRACTION100
2.92-3.010.33551480.25632720X-RAY DIFFRACTION100
3.01-3.110.31761410.25882709X-RAY DIFFRACTION99.96
3.11-3.220.31111370.26782734X-RAY DIFFRACTION99.97
3.22-3.340.31461680.23482688X-RAY DIFFRACTION99.96
3.35-3.50.28731500.21432714X-RAY DIFFRACTION100
3.5-3.680.25421460.18352716X-RAY DIFFRACTION99.97
3.68-3.910.20221390.16752753X-RAY DIFFRACTION100
3.91-4.210.22331450.15922734X-RAY DIFFRACTION100
4.21-4.640.20241610.13922760X-RAY DIFFRACTION100
4.64-5.310.20221500.13652769X-RAY DIFFRACTION100
5.31-6.690.19211400.16622817X-RAY DIFFRACTION100
6.69-78.230.1981420.16652944X-RAY DIFFRACTION99.84
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.366898136095.402731362221.426121597748.973544109853.560854869683.09996197606-0.3144449790760.4398559508910.707733621824-0.113523619340.07441729750361.19729888469-0.280744960805-0.1764461380340.2528395730160.5008749361410.0412958269412-0.07524966923630.5679875735930.05491914277290.497701076203-16.482284577216.9649447941-18.9422156664
25.32548581301-2.039132300410.2883556994381.04531064160.2003600525947.47599971457-0.08812682001790.3012888882420.585850881162-0.09294447645110.0011921023901-0.721473359501-1.317007073020.6205549740680.1537269509260.610528276869-0.04644741336040.004953952620760.4404379989650.06703358553510.574384857553-1.3319995968829.8408561911-19.601745247
31.072789609170.1094986303970.1986792284342.69455805754-0.5433281464752.67409483092-0.1288382431910.1909646593150.04613541264660.2413303064440.0206161054399-0.0844978422786-0.1244715280480.1201670880140.1644948980710.4095879068520.0244016863509-0.003692821014190.4249254366840.01054843215950.425719099854-4.6669003033918.180726626-15.167730046
45.66525402958-0.227525530512-3.438822485042.865473374780.5580694486018.139505619910.03718974133740.005596517700880.2218449117750.131744323552-0.105180223404-0.562955443373-0.2647670847410.6633857458480.05236415324450.507433572875-0.0673284393475-0.08398392104680.515424958540.07099061638180.7000782018345.5775655074224.1069600163-15.4226716314
59.333001292875.402435997744.738924220433.53255004083.74534087095.078174030690.546551802542-0.2056063477930.304268843374-0.161343332368-0.3826192538660.1826831756090.0402334319105-0.740155287435-0.1929889120260.511922166010.09026865485330.02520227325460.5853595033330.06840451618130.522411419058-7.8702009185414.6127112812-34.1517272669
64.7995590404-0.513056791846-0.8035246958843.4365473001-0.4591584958332.392058910860.1089965882050.267019367182-0.0821950724663-0.242169344393-0.117395527262-0.2634626859030.29717532897-0.03604271758860.01661434629410.3984672463940.03247030034590.02810559523640.379345925131-0.03226949218390.374317600111-4.680280944-1.0191924435-26.819619025
75.9012220799-2.819724611591.318166660011.45207208737-0.1557653534396.319788942460.04579022748860.03092524703280.2386901517710.215739988451-0.05675358958870.3172456248970.141007382203-0.57803241940.01815784615810.587416280376-0.1267532038910.09391623882740.628908298460.02411966572450.780800555942-24.2028535965-4.32141356086-20.3660223624
83.094220501393.063728333070.1656577866676.11495802167-1.020154200891.44772754723-0.09052986098610.07863897267720.936930543650.2626963930910.2720089730981.27434772192-0.296368645119-0.421027425755-0.1652935463480.5508200477590.135762952180.1695753701950.44202623571-0.01065519998580.652747555434-38.376680436443.2800572424-32.7304272962
91.39886059790.2684167455081.744950239822.313415398692.167793044973.64540539161-0.161454583366-0.209207690104-0.3731808007470.2465978726820.3017733562390.6432227591040.0833700169389-0.712970035714-0.1521320121760.5230466520630.02974793563950.1729598430850.6568127576470.03763067251720.767947426988-43.942353468825.6726288213-25.7960406198
101.83105969199-0.6862127622390.1722908727013.41688270283-2.014932300144.67838999108-0.05715574613820.173456701584-0.28067532163-0.2621417941050.1088794535540.2039421149340.267279957043-0.326965627437-0.07628155831970.421422713572-0.03504972924550.06914457381080.432131637604-0.02506446019890.607011774953-39.35628619625.2199361544-35.3441031174
114.545364067860.8135308531486.089462050594.92406470241-1.618120678889.867650498840.0711337950397-0.0705123300688-0.8350294496540.3611224874920.3563986718950.006141253244990.325924896727-0.0170797356129-0.3539363666490.538448922301-0.0238900245240.1181915943520.433185634091-0.01453082872480.587738998171-31.667177097817.9530965197-22.8702390325
121.9960288671-0.244127578469-0.2303566337161.781224468090.211281228232.18497595338-0.0231240751167-0.1095156646960.1157039060380.0797501932232-0.0572408213256-0.015151216907-0.1677088968660.1879935307040.08343475179970.395100745452-0.001735198609120.0354434897580.364864122237-0.007400011836810.452361167699-17.62426224641.7137519228-32.3876514261
134.56421211669-1.33177630419-1.148288524222.072984448081.012742278451.76386171822-0.112483782775-0.361351527154-0.1089211437140.4679881828030.183736894189-0.1615724066050.6321783886270.0123572784689-0.06112764899840.673443484759-0.0368791661822-0.05402618382680.422062216792-0.02484805852640.407758466266-0.525799168417-8.166292051723.55966466939
145.664006804441.527594352992.781763654.155143006382.33086037027.973145083690.1059926876150.1840176035160.293405610031-0.02409614738990.0282650653737-0.5587048191690.004696281441770.4989677799-0.1635352310440.4486144563040.057450550666-0.007300997387650.389260362678-0.02964123098030.52165308974412.8696181379-5.96958851442-2.24775549364
154.91133366547-2.286297617651.223332575434.38409706824-1.670964926710.847839942203-0.243101214163-0.501122432916-0.1097437255280.4700494528650.172740167011-0.113699308640.19024188262-0.3143085419540.07322807911160.82271383892-0.152343416348-0.01758803414610.553531891249-0.1012129242690.422726016833-3.469079795042.2020702024614.822266627
163.471973154010.688177260211-0.5272175686012.02813399342-2.026725604934.73480460733-0.0389226614182-0.4434008274770.3116535776130.911856059696-0.1461410589970.0497106856119-0.474739471978-0.1473005727250.1425384441660.871088330946-0.0570863939923-0.05836797939040.556600346185-0.1272799784930.485221273184-3.5899836861213.418613773814.1045483992
172.528017505370.5257132395641.531136160171.52528079574-0.209045848952.378924644-0.2321871931650.1148338042280.3860098500420.361595083454-0.098137047229-0.182249302229-0.258248373624-0.05085235072690.3276924362830.796047459204-0.0105856391425-0.174851732070.418363222708-0.04978538889470.574334616775-0.064388807587116.71788687869.83998859708
182.691236210321.865072725091.352990176776.78714773304-1.189470424562.20216723295-0.1241137455550.02680251701830.4567015554790.6159569423380.3669436448910.960732165968-0.68501498888-0.758943652454-0.1761715589880.7143876620250.04200219647310.1638705576380.771449157246-0.01498296347460.731155689233-27.27006049889.1773322023412.0024534391
196.103078652673.00332758498-3.785589547326.810229262580.8102145757033.70599023897-0.6796693924111.517479440341.34637458142-0.01224103535140.5253485310370.866270965212-1.24851735131-0.7845384992620.1858906948210.6749772907270.05353105508420.02950543861320.737879248480.2449918519140.644395351805-36.039021776741.3829158629-68.6860153931
208.08465675915-5.492307988573.720757497993.77037180462-2.087157190725.37016465929-0.1483606465250.2771732053460.625884718956-0.08527885296210.174450650793-0.640118826315-0.5100322768040.781629918884-0.02326289022510.641254105446-0.1735175847840.05575151490210.766047339418-0.001937753463750.577720961194-8.6368100056732.1664453935-61.9084423621
214.51104980842-3.624790659152.455873472643.99272093347-2.33349113093.285931591560.361924871015-0.2326990990640.544091691543-0.534978787912-0.0323810325425-0.4178977794860.2953371105070.189082712841-0.338093241210.620518841714-0.1121993912160.08136018173350.579333943928-0.07052111651940.582457462526-8.4155432136622.0129409283-62.0262370583
223.36060746361-0.737443269541-0.1193093330062.245673900650.4944799363331.371571425390.1182574036780.02569830781-0.04090862267070.08496773626710.01508917587610.237407330506-0.04149591863250.0562167968542-0.1779009657960.610232795998-0.01287498502460.03958027292970.5389483408180.04946352620450.461947833207-18.075975491927.1605574162-56.5803266678
232.010304037591.43827030049-1.374167355599.827518705410.7949679423965.90437754118-0.006682439415460.0706969629436-0.1867771835350.74226624471-0.0504325768486-0.411205881110.3958699947090.4602362722830.03609043457520.5893334279850.0367303428132-0.04832973364820.5965650386890.03251482109510.535321830751-8.478065520321.0334931559-48.8646519313
242.472316786591.12043356811.440365794652.895698205153.068520346153.656121857290.158560150215-0.128105340557-0.193921372979-0.172112481853-0.1060500715130.1058985141130.271479739250.240332178593-0.09020475391170.573134612203-0.0293901273765-0.01872495535650.5434057118520.03822969623070.459122668808-14.985217666815.9488035176-57.3499791729
254.79677826618-4.985199048324.095938016935.21534010224-4.43562098675.127628148770.2019018403450.4497912237110.408468284471-0.120147417351-0.478819122885-0.06370975930980.03606133815070.1608579655070.248130393970.602975054241-0.0429553790809-0.008300754929710.6875500943450.001325176772350.535388639149-27.16830804722.2940530918-73.5010548638
263.566923979590.576756347712-3.503896755144.1588299811.424563414484.61106429824-0.1742122274620.4584162941690.0580821347928-0.221378409297-0.1113608191840.1708979470690.0548849237802-0.8113891085380.2531508228570.35966263187-0.0590181203153-0.06318785333520.526074283640.03717856963420.43416195508-35.722607166527.5956429899-62.7932162734
275.138208831621.85180194101-2.788075486224.01534534883-4.123309444414.37640551863-0.6505965722271.18496541246-0.26890337355-0.6746452912910.4664978779810.1333688967160.786659969861-1.301749510580.03334267692720.675306378659-0.0920454465613-0.0632805749740.902684612978-0.1225781097910.577378141888-45.441526649522.7693767968-63.9219063787
285.11285065598-0.959568136732-7.058358050910.2313271789281.384124789959.7315046795-0.746959665446-0.44602901155-0.6864056906010.31814116493-0.03043633989260.1652962214260.9526341962110.05844702539910.830674419010.557740796146-0.07528663100590.08062293713570.614497344357-0.0296487840640.506737214998-33.303445460212.2985364091-58.6183270984
292.172775454580.711603573413-1.417746358126.86093414311-2.326639769086.775450531570.07010708595450.862041410951-0.1616545178930.2177715943170.05558990798290.54969650452-0.212293753474-1.03453321117-0.2162366548840.425361531991-0.03760575458650.03636724271010.808176688859-0.05651822049950.656739223676-46.87430291627.0276533077-57.1868832053
307.87516854697-0.9123867015342.089287129029.53138359002-0.494898542289.66556446884-0.2841795346070.5447809670481.14716203807-0.114807578685-0.2944465296710.609476321755-0.93321339958-0.9268996370070.5902750836190.7348741295290.203067979261-0.06793960710730.9577298085040.1075615476710.897065384515-45.81031670843.8930721607-62.3094902298
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 37 )AA1 - 371 - 37
22chain 'A' and (resid 38 through 56 )AA38 - 5638 - 56
33chain 'A' and (resid 57 through 87 )AA57 - 8757 - 87
44chain 'A' and (resid 88 through 151 )AA88 - 15188 - 151
55chain 'A' and (resid 152 through 168 )AA152 - 168152 - 168
66chain 'A' and (resid 169 through 276 )AA169 - 276169 - 276
77chain 'A' and (resid 277 through 309 )AA277 - 309277 - 306
88chain 'B' and (resid 1 through 37 )BD1 - 371 - 37
99chain 'B' and (resid 38 through 56 )BD38 - 5638 - 56
1010chain 'B' and (resid 57 through 128 )BD57 - 12857 - 128
1111chain 'B' and (resid 129 through 151 )BD129 - 151129 - 151
1212chain 'B' and (resid 152 through 298 )BD152 - 298152 - 298
1313chain 'C' and (resid 1 through 87 )CG1 - 871 - 87
1414chain 'C' and (resid 88 through 151 )CG88 - 15188 - 151
1515chain 'C' and (resid 152 through 183 )CG152 - 183152 - 183
1616chain 'C' and (resid 184 through 231 )CG184 - 231184 - 231
1717chain 'C' and (resid 232 through 276 )CG232 - 276232 - 276
1818chain 'C' and (resid 277 through 306 )CG277 - 306277 - 306
1919chain 'D' and (resid 1 through 17 )DJ1 - 171 - 17
2020chain 'D' and (resid 18 through 37 )DJ18 - 3718 - 37
2121chain 'D' and (resid 38 through 56 )DJ38 - 5638 - 56
2222chain 'D' and (resid 57 through 87 )DJ57 - 8757 - 87
2323chain 'D' and (resid 88 through 112 )DJ88 - 11288 - 112
2424chain 'D' and (resid 113 through 151 )DJ113 - 151113 - 151
2525chain 'D' and (resid 152 through 168 )DJ152 - 168152 - 168
2626chain 'D' and (resid 169 through 210 )DJ169 - 210169 - 210
2727chain 'D' and (resid 211 through 231 )DJ211 - 231211 - 231
2828chain 'D' and (resid 232 through 253 )DJ232 - 253232 - 253
2929chain 'D' and (resid 254 through 276 )DJ254 - 276254 - 276
3030chain 'D' and (resid 277 through 298 )DJ277 - 298277 - 298

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