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- PDB-8ohj: PanDDA analysis group deposition -- CdaA in complex with fragment... -

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Basic information

Entry
Database: PDB / ID: 8ohj
TitlePanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry G08
ComponentsCyclic di-AMP synthase CdaA
KeywordsTRANSFERASE / diadenylate cyclase
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
Chem-RDJ / Cyclic di-AMP synthase CdaA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsGarbers, T.B. / Neumann, P. / Wollenhaupt, J. / Weiss, M.S. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
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
DepositionMar 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)33,6164
Polymers33,3622
Non-polymers2542
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-13 kcal/mol
Surface area14460 Å2
Unit cell
Length a, b, c (Å)118.780, 39.230, 68.370
Angle α, β, γ (deg.)90.000, 95.630, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-442-

HOH

21B-518-

HOH

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Components

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


Mass: 16681.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: cdaA, ybbP, BSU01750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45589, diadenylate cyclase
#2: Chemical ChemComp-RDJ / N-ethyl-2-{[5-(propan-2-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetamide


Mass: 229.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 0.1 M Magnesium chloride 30 % (v/v) PEG 400 20 % (v/v) DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 171592 / % possible obs: 96.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 17.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.074 / Net I/σ(I): 7.63
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.23-1.262.086124260.2322.5971
1.26-1.31.613121950.3342.0111
1.3-1.331.341119740.4091.6761
1.33-1.381.151114270.4561.4451
1.38-1.420.908113070.5681.1331
1.42-1.470.754109820.6280.9371
1.47-1.530.555106260.7520.6921
1.53-1.590.407101720.8430.5091
1.59-1.660.29696630.910.3721
1.66-1.740.22494770.950.2791
1.74-1.830.16689600.9650.2071
1.83-1.940.10785400.9850.1341
1.94-2.080.0778270.9930.0881
2.08-2.250.05674550.9960.0691
2.25-2.460.04569080.9960.0551
2.46-2.750.03861940.9970.0471
2.75-3.180.03153140.9980.0391
3.18-3.890.02646770.9980.0321
3.89-5.50.02535350.9980.031

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→46.96 Å / SU ML: 0.2211 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.3552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2067 2097 2.32 %
Rwork0.1814 88465 -
obs0.1819 90562 96.42 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.25 Å2
Refinement stepCycle: LAST / Resolution: 1.22→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 16 316 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362349
X-RAY DIFFRACTIONf_angle_d0.63193188
X-RAY DIFFRACTIONf_chiral_restr0.0612386
X-RAY DIFFRACTIONf_plane_restr0.0043413
X-RAY DIFFRACTIONf_dihedral_angle_d5.2546336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.55971270.53945356X-RAY DIFFRACTION87.97
1.25-1.280.51661370.46075746X-RAY DIFFRACTION94.49
1.28-1.310.41241370.39175773X-RAY DIFFRACTION95.29
1.31-1.350.34341390.34425853X-RAY DIFFRACTION95.99
1.35-1.390.34251380.31575828X-RAY DIFFRACTION95.46
1.39-1.440.32021390.29175850X-RAY DIFFRACTION96.8
1.44-1.50.30951400.27025901X-RAY DIFFRACTION96.94
1.5-1.570.25731410.2065944X-RAY DIFFRACTION97.27
1.57-1.650.24681390.1835881X-RAY DIFFRACTION96.74
1.65-1.760.19461420.16645964X-RAY DIFFRACTION97.48
1.76-1.890.1691420.15276000X-RAY DIFFRACTION98.01
1.89-2.080.16311420.13885981X-RAY DIFFRACTION97.67
2.08-2.390.18691440.13836076X-RAY DIFFRACTION98.84
2.39-30.18371430.1586060X-RAY DIFFRACTION98.32
3.01-46.960.17911470.16866252X-RAY DIFFRACTION98.89

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