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- PDB-8ogk: Crystal structure of CdaA from Bacillus subtilis co-crystallized ... -

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Basic information

Entry
Database: PDB / ID: 8ogk
TitleCrystal structure of CdaA from Bacillus subtilis co-crystallized with DMSO
ComponentsCyclic di-AMP synthase CdaA
KeywordsUNKNOWN FUNCTION / octamer / unkown function
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: 1.18 Å
AuthorsGarbers, T.B. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
CitationJournal: To Be Published
Title: Crystal structure of CdaA from Bacillus subtilis co-crystallized with DMSO
Authors: Garbers, T.B. / Neumann, P. / Wollenhaupt, J. / Weiss, M. / Ficner, R.
History
DepositionMar 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: 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)33,6997
Polymers33,3622
Non-polymers3375
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-10 kcal/mol
Surface area14390 Å2
Unit cell
Length a, b, c (Å)118.650, 39.240, 67.980
Angle α, β, γ (deg.)90.000, 94.990, 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
11A-473-

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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.94 %
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 20 % (v/v) DMSO
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.68879 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.68879 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 101314 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.034 / Net I/σ(I): 19.96
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.18-1.281.773216310.6471.9131
1.28-1.380.888158280.8660.9591
1.38-1.580.31210880.9780.3351
1.58-80.0244243110.0261
8-140.0232760.9990.0251
14-170.023290.9990.0261
17-500.025310.9990.0291

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→46.58 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1938 5064 5 %
Rwork0.1746 96198 -
obs0.1756 101262 98.55 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.58 Å2
Refinement stepCycle: LAST / Resolution: 1.18→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 17 174 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722368
X-RAY DIFFRACTIONf_angle_d0.98973205
X-RAY DIFFRACTIONf_chiral_restr0.0692386
X-RAY DIFFRACTIONf_plane_restr0.008414
X-RAY DIFFRACTIONf_dihedral_angle_d14.5494890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.38781680.41783182X-RAY DIFFRACTION98.21
1.19-1.210.44231670.39853167X-RAY DIFFRACTION98.35
1.21-1.220.4091650.3883134X-RAY DIFFRACTION97.52
1.22-1.240.4011660.36183145X-RAY DIFFRACTION97.67
1.24-1.250.38461660.36663156X-RAY DIFFRACTION97.71
1.25-1.270.39781680.35093184X-RAY DIFFRACTION97.41
1.27-1.290.32731660.31093151X-RAY DIFFRACTION97.5
1.29-1.310.31521680.29893182X-RAY DIFFRACTION97.72
1.31-1.330.28591660.27373155X-RAY DIFFRACTION98.05
1.33-1.350.3171670.2743174X-RAY DIFFRACTION97.95
1.35-1.370.32351660.25773152X-RAY DIFFRACTION97.67
1.37-1.40.27441670.24273173X-RAY DIFFRACTION97.78
1.4-1.430.25221650.223127X-RAY DIFFRACTION97.31
1.43-1.460.26991680.21443217X-RAY DIFFRACTION98.43
1.46-1.490.23781690.19753216X-RAY DIFFRACTION99.18
1.49-1.520.21841690.18823208X-RAY DIFFRACTION98.77
1.52-1.560.21391690.17383215X-RAY DIFFRACTION99.56
1.56-1.60.2411700.16483235X-RAY DIFFRACTION99.5
1.6-1.650.18611700.15283216X-RAY DIFFRACTION99.62
1.65-1.70.20871720.14523275X-RAY DIFFRACTION99.74
1.7-1.760.19421690.14483218X-RAY DIFFRACTION99.68
1.76-1.830.16871710.14173237X-RAY DIFFRACTION99.65
1.83-1.920.18581710.13983247X-RAY DIFFRACTION99.56
1.92-2.020.18411710.13913252X-RAY DIFFRACTION99.53
2.02-2.140.17121710.13353243X-RAY DIFFRACTION99.45
2.14-2.310.1591720.13373270X-RAY DIFFRACTION99.25
2.31-2.540.18891670.14653187X-RAY DIFFRACTION97.81
2.54-2.910.19791710.16033232X-RAY DIFFRACTION98.27
2.91-3.670.15621730.17193300X-RAY DIFFRACTION99.54
3.67-46.580.18471760.18933348X-RAY DIFFRACTION98.16

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