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

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Basic information

Entry
Database: PDB / ID: 8ogu
TitlePanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry C07
ComponentsCyclic di-AMP synthase CdaA
KeywordsTRANSFERASE / diadenylate cyclase
Function / homology
Function and homology information


diadenylate cyclase activity / diadenylate cyclase / 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: 1.41 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: To Be Published
Title: PanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry C07
Authors: Garbers, T.B. / Neumann, P. / Wollenhaupt, J. / Weiss, M.S. / 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)33,6815
Polymers33,3622
Non-polymers3193
Water6,017334
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 area14360 Å2
Unit cell
Length a, b, c (Å)118.880, 39.070, 68.110
Angle α, β, γ (deg.)90.000, 95.310, 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-471-

HOH

21B-518-

HOH

31B-520-

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-VN9 / 3,4-dihydro-1~{H}-quinolin-2-one


Mass: 147.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO / 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.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 47.89 %
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: 1.39→50 Å / Num. obs: 119643 / % possible obs: 97.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 19.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.098 / Net I/σ(I): 6.29
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.39-1.432.33187920.1872.8941
1.43-1.471.76285700.2652.191
1.47-1.511.3384670.3791.6561
1.51-1.550.96380920.4851.2031
1.55-1.610.76478350.5910.9591
1.61-1.660.54875030.7580.6851
1.66-1.720.46473630.8230.5751
1.72-1.790.34871150.8750.4311
1.79-1.870.25468460.9270.3151
1.87-1.970.17966180.9610.2241
1.97-2.070.12560790.9780.1581
2.07-2.20.09859560.9880.1221
2.2-2.350.07855400.9910.0971
2.35-2.540.06652080.9920.0821
2.54-2.780.05847130.9930.0731
2.78-3.110.04741800.9950.0591
3.11-3.590.04138300.9950.0511
3.59-4.40.03831990.9960.0461
4.4-6.220.03623930.9960.0461

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→42.68 Å / SU ML: 0.2067 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6606
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 2099 3.59 %
Rwork0.1727 56337 -
obs0.1739 58436 97.67 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.69 Å2
Refinement stepCycle: LAST / Resolution: 1.41→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 23 334 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552364
X-RAY DIFFRACTIONf_angle_d0.79943206
X-RAY DIFFRACTIONf_chiral_restr0.0674386
X-RAY DIFFRACTIONf_plane_restr0.0058413
X-RAY DIFFRACTIONf_dihedral_angle_d10.047338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.450.3661270.41783423X-RAY DIFFRACTION88.73
1.45-1.480.41031370.34953704X-RAY DIFFRACTION97.93
1.48-1.520.38071400.29443749X-RAY DIFFRACTION97.86
1.52-1.570.30211390.2583727X-RAY DIFFRACTION97.87
1.57-1.620.28331370.23183677X-RAY DIFFRACTION96.88
1.62-1.680.27581400.2093736X-RAY DIFFRACTION97.46
1.68-1.740.23191390.19383753X-RAY DIFFRACTION98.41
1.74-1.820.25021400.17983758X-RAY DIFFRACTION97.99
1.82-1.920.21471420.14893796X-RAY DIFFRACTION98.94
1.92-2.040.18211410.13363778X-RAY DIFFRACTION98.49
2.04-2.20.17441420.13433812X-RAY DIFFRACTION98.95
2.2-2.420.1691430.13733833X-RAY DIFFRACTION99.45
2.42-2.770.20841420.15343816X-RAY DIFFRACTION98.9
2.77-3.490.18671430.16763834X-RAY DIFFRACTION98.61
3.49-42.680.19461470.17243941X-RAY DIFFRACTION98.6

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