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- PDB-8ogm: Crystal structure of CdaA from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 8ogm
TitleCrystal structure of CdaA from Bacillus subtilis
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
Cyclic di-AMP synthase CdaA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGarbers, T.B. / Neumann, P. / Weiss, M.S. / Wollenhaupt, J. / 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 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 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

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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


Theoretical massNumber of molelcules
Total (without water)33,3622
Polymers33,3622
Non-polymers00
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-10 kcal/mol
Surface area14540 Å2
Unit cell
Length a, b, c (Å)119.360, 39.480, 68.230
Angle α, β, γ (deg.)90.000, 95.370, 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-342-

HOH

21B-429-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes pH 7.5 0.2 M Magnesium chloride 30% (v/v) PEG 400
PH range: 7.5

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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: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 117659 / % possible obs: 91.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.042 / Net I/σ(I): 13.75
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.131.61380660.6051.8621
1.13-1.161.11780240.7071.2941
1.16-1.190.86479000.7961.0031
1.19-1.230.68275200.8310.7921
1.23-1.270.56776270.8910.6531
1.27-1.310.41874990.9320.4821
1.31-1.360.32173730.9530.371
1.36-1.420.24270520.9690.281
1.42-1.480.16565000.9840.1921
1.48-1.560.11766540.9920.1351
1.56-1.640.08563250.9950.0981
1.64-1.740.06460000.9970.0741
1.74-1.860.04956260.9970.0571
1.86-2.010.03851030.9980.0451
2.01-2.20.03247170.9980.0371
2.2-2.460.02844650.9980.0331
2.46-2.840.02639230.9990.031
2.84-3.480.02432780.9990.0281
3.48-4.920.02225080.9990.0261

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→37.47 Å / SU ML: 0.1616 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2011 5912 5.03 %
Rwork0.171 111715 -
obs0.1725 117627 91.5 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.94 Å2
Refinement stepCycle: LAST / Resolution: 1.1→37.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 0 357 2676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112348
X-RAY DIFFRACTIONf_angle_d1.21013177
X-RAY DIFFRACTIONf_chiral_restr0.0872385
X-RAY DIFFRACTIONf_plane_restr0.0114409
X-RAY DIFFRACTIONf_dihedral_angle_d14.7325888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.42431840.4043364X-RAY DIFFRACTION84.74
1.11-1.130.3752170.38433508X-RAY DIFFRACTION85.81
1.13-1.140.39791970.36523452X-RAY DIFFRACTION86.16
1.14-1.150.39371740.35913517X-RAY DIFFRACTION87.09
1.15-1.170.36641800.34173553X-RAY DIFFRACTION87.75
1.17-1.180.33831640.32043599X-RAY DIFFRACTION88.42
1.18-1.20.3581870.3123547X-RAY DIFFRACTION87.43
1.2-1.220.31511860.30053344X-RAY DIFFRACTION83.25
1.22-1.240.33631770.28283697X-RAY DIFFRACTION90.7
1.24-1.260.34381820.27183654X-RAY DIFFRACTION90.28
1.26-1.280.2461830.24473703X-RAY DIFFRACTION90.69
1.28-1.30.27721840.2333726X-RAY DIFFRACTION91.72
1.3-1.330.23831940.22113737X-RAY DIFFRACTION92.13
1.33-1.360.2631890.21593831X-RAY DIFFRACTION93.55
1.36-1.390.2561770.20093788X-RAY DIFFRACTION93.49
1.39-1.420.24242090.19763797X-RAY DIFFRACTION93.34
1.42-1.450.21351950.1833746X-RAY DIFFRACTION91.8
1.45-1.490.21591950.17773566X-RAY DIFFRACTION88.51
1.49-1.540.20882230.15623850X-RAY DIFFRACTION94.99
1.54-1.590.19272060.13623883X-RAY DIFFRACTION95.09
1.59-1.640.18512110.13653869X-RAY DIFFRACTION95.37
1.64-1.710.17432040.13283899X-RAY DIFFRACTION95.57
1.71-1.790.19512070.13643858X-RAY DIFFRACTION95.11
1.79-1.880.17121980.14443883X-RAY DIFFRACTION94.84
1.88-20.17192000.13573758X-RAY DIFFRACTION92.58
2-2.150.15511990.13843753X-RAY DIFFRACTION91.4
2.15-2.370.16032580.13643905X-RAY DIFFRACTION96.68
2.37-2.710.16292150.15623967X-RAY DIFFRACTION96.34
2.71-3.420.19792030.16753954X-RAY DIFFRACTION95.3
3.42-37.470.20292140.16564007X-RAY DIFFRACTION94.39

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