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- PDB-9g0g: BsCdaA in complex with Compound 7 -

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Basic information

Entry
Database: PDB / ID: 9g0g
TitleBsCdaA in complex with Compound 7
ComponentsCyclic di-AMP synthase CdaA
KeywordsTRANSFERASE / CdaA / Cyclic-di-AMP
Function / homology
Function and homology information


diadenylate cyclase / diadenylate cyclase activity / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane
Similarity search - Function
Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / : / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-TJ9 / Cyclic di-AMP synthase CdaA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsNeumann, P. / Ficner, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystallographic fragment screen of the c-di-AMP-synthesizing enzyme CdaA from Bacillus subtilis.
Authors: Garbers, T. / Neumann, P. / Wollenhaupt, J. / Dickmanns, A. / Weiss, M.S. / Ficner, R.
History
DepositionJul 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic di-AMP synthase CdaA
B: Cyclic di-AMP synthase CdaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,72627
Polymers33,6202
Non-polymers2,10625
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-41 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.500, 39.230, 67.600
Angle α, β, γ (deg.)90.000, 94.290, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11B-309-

CL

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cyclic di-AMP synthase CdaA / c-di-AMP synthase / Diadenylate cyclase / DAC


Mass: 16810.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GP are part of the precission protease site / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: cdaA, ybbP, BSU01750 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45589, diadenylate cyclase

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Non-polymers , 5 types, 191 molecules

#2: Chemical ChemComp-TJ9 / ~{N}-[5-(2-azanyl-1,3-thiazol-4-yl)-4-methyl-1,3-thiazol-2-yl]ethanamide


Mass: 254.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10N4OS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 8.0, 200 mM MgCl2 30% (v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5406 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 8, 2021
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.7→23.74 Å / Num. obs: 32367 / % possible obs: 93.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.059 / Net I/σ(I): 18.36
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.7-1.80.61448000.8810.6791
1.8-1.90.30539550.9680.3351
1.9-2.10.14358930.9920.1571
2.1-80.044173660.9990.0481
8-140.0352850.9990.0391
14-170.043280.9990.0561
17-502.386400.732.8531

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→21.54 Å / SU ML: 0.2237 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2041 1619 5.01 %
Rwork0.1736 30694 -
obs0.1751 32313 93.83 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 112 166 2606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652469
X-RAY DIFFRACTIONf_angle_d0.77813322
X-RAY DIFFRACTIONf_chiral_restr0.0555388
X-RAY DIFFRACTIONf_plane_restr0.0078422
X-RAY DIFFRACTIONf_dihedral_angle_d14.5622918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.45221270.39442357X-RAY DIFFRACTION89.26
1.75-1.810.28931300.21862479X-RAY DIFFRACTION90.65
1.81-1.870.2371310.20172478X-RAY DIFFRACTION91.61
1.87-1.950.20621300.19442494X-RAY DIFFRACTION91.91
1.95-2.030.22431310.17162495X-RAY DIFFRACTION92.76
2.03-2.140.21261340.16442531X-RAY DIFFRACTION93.48
2.14-2.280.21331340.16582557X-RAY DIFFRACTION93.93
2.28-2.450.23471370.16972601X-RAY DIFFRACTION94.9
2.45-2.70.22591370.17412611X-RAY DIFFRACTION95.68
2.7-3.090.20261390.16762630X-RAY DIFFRACTION96.55
3.09-3.880.17231420.15672697X-RAY DIFFRACTION97.66
3.89-21.540.17741470.172764X-RAY DIFFRACTION97.39
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)
11.05872128075-0.0663334073674-0.6906206190620.7912449920310.1868508146370.444908180220.2447700965830.0499606338321-0.546592511618-0.134438879659-0.031590973928-0.06584342274870.760868850350.09812861649950.008436226040240.288671161661-0.0102485006472-0.0358283531930.1924755412940.01437861037030.30480859879819.842635659-20.745798967816.3608593052
22.732320569930.614632431329-1.082894501831.68498453492-0.02604517311180.3479652047010.116394069136-0.14175223550.1453867508620.116405019736-0.01836482239570.0142574578175-0.08705166976730.06353845280690.001618426433210.219023922864-0.03414883747080.005598005990630.180185072859-0.02351698409490.18658941441514.0038909075-8.6123033987117.7703877735
32.122677955621.55159031221-1.057788712761.09916901622-0.867059592091.213783600380.1483483745650.7656359324381.1804803764-0.09794860145610.2300754037960.527260670307-0.129563798521-0.1967113085560.1595431678310.258080793605-0.02939398715480.007371688205490.3470280179950.1178186800190.28456172975523.38814000772.326242060968.08241296387
40.43506565115-0.413783049398-0.05125083588410.4222502308950.06457373990540.2191331372270.09002314943970.2141754739940.173325947695-0.07504670018080.0206751002001-0.105770448954-0.1965341022660.1742056733710.007631430045330.222327116022-0.04797869605930.01405721088850.1861787279670.0033624408760.23049398796324.2459537488-2.5509131711113.2034111241
50.25380403596-0.159635901563-0.0003028006412180.4833651473160.254106283490.2120254616950.0371799605280.4102512955960.152178272775-0.229211168324-0.0331884271683-0.143102976972-0.1560769152370.2004508517562.09871489752E-70.258062518155-0.02759738626610.0106507454440.2953710284190.009692066600160.22283394476727.7087597398-8.439396283217.23436387964
60.180398158456-0.0854572555378-0.004984316102220.140762740015-0.1731359291530.205023500559-0.17931604799-0.550294646581-0.2111876965120.503700988384-0.0816837911112-0.4311996370160.3536875945490.2922534352287.51648979462E-70.3168736738590.0157300246129-0.03030314468580.4068424535470.0738607438060.34270210971729.7642763159-17.621319063817.4350651078
70.630003832113-0.3597336017120.240896029540.485423415385-0.04990431476860.451726519502-0.1271504336170.1144689112980.439525274866-0.0475762870147-0.0130024935435-0.0236829192433-0.798694185919-0.258955487006-0.0258974956760.3265695902330.0142833970753-0.006600173162110.1897301293530.01359039177570.332538657129-7.50346076135-5.4540469960321.3437247049
81.570985167370.2428021124740.1719072274150.537994509852-0.0703954614430.3135201104480.0715785500312-0.200368985831-0.0001550155311670.04325749772220.0551219776430.04560777597-0.074058157648-0.169584039608-2.93075997214E-70.221119969662-0.0264416132956-0.01702096780770.2524942732730.01757521532750.200398867536-5.79472255369-21.810472805223.4621543529
91.79995179781-0.100120220045-0.3814803988351.73131424887-0.996120928320.5331119802890.02622274431090.130203868760.0195564510050.1136319812680.0546657810151-0.01271228920740.0627527858584-0.09444447286714.02145670333E-70.202694394684-0.0254525528171-0.001994646687710.204371132690.005166713078190.1931149867191.08154494445-15.970338250118.7120637101
100.162866406365-0.137687777439-0.2386198551030.3607608139760.2446691467230.142924786685-0.1468546624851.41474100002-0.514768416314-0.1651575201330.294726414056-0.0116261838492-0.0648191964980.1031494962890.003183531321280.227160363998-0.0514494600389-0.05251220671960.406454404737-0.03080145268290.286183729531-13.4392207697-29.36533466814.9019485073
111.574344770130.1826491615570.7711544744471.02905829443-0.5098061760510.5058292299540.09774934521690.0186499360428-0.08331092220920.01265166147850.002396349122920.0948142351593-0.0517917485476-0.2557781171276.40029481534E-80.230094785125-0.0171103629613-0.006200408635490.2261561956530.02575454761120.214654952206-14.9512073635-21.413082967416.9294006229
120.2902994521720.1809682436740.06013639742470.4273922889370.3700543032440.297759510476-0.0586852902577-0.6538800165970.4106413922450.585436186026-0.07379120879730.472850097074-0.546491957528-0.27681342269-0.04046635298950.400513631876-0.01697339583440.1164971772360.411997402534-0.07418747933020.423596538392-16.5096843974-9.0194295634924.3898966938
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 103 through 126 )AA103 - 1261 - 24
22chain 'A' and (resid 127 through 183 )AA127 - 18325 - 81
33chain 'A' and (resid 184 through 201 )AA184 - 20182 - 99
44chain 'A' and (resid 202 through 221 )AA202 - 221100 - 119
55chain 'A' and (resid 222 through 241 )AA222 - 241120 - 139
66chain 'A' and (resid 242 through 254 )AA242 - 254140 - 152
77chain 'B' and (resid 102 through 126 )BM102 - 1261 - 25
88chain 'B' and (resid 127 through 146 )BM127 - 14626 - 45
99chain 'B' and (resid 147 through 183 )BM147 - 18346 - 82
1010chain 'B' and (resid 184 through 201 )BM184 - 20183 - 100
1111chain 'B' and (resid 202 through 241 )BM202 - 241101 - 140
1212chain 'B' and (resid 242 through 255 )BM242 - 255141 - 154

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