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

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Basic information

Entry
Database: PDB / ID: 8ohe
TitlePanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry F03
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
N-(3-fluorophenyl)-2-(2-methoxyethoxy)acetamide / Cyclic di-AMP synthase CdaA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 F03
Authors: Garbers, T.B. / Neumann, P. / Wollenhaupt, J. / Weiss, M.S. / Ficner, R.
History
DepositionMar 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 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)33,6144
Polymers33,3622
Non-polymers2522
Water5,891327
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 area14280 Å2
Unit cell
Length a, b, c (Å)118.880, 39.230, 68.200
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-484-

HOH

21B-519-

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-RAY / N-(3-fluorophenyl)-2-(2-methoxyethoxy)acetamide


Mass: 227.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14FNO3 / 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.: 327 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
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: 1.15→50 Å / Num. obs: 201032 / % possible obs: 94.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 15.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.056 / Net I/σ(I): 9.65
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.16-1.191.658113220.2882.1981
1.19-1.221.561131510.3692.0121
1.22-1.261.356143270.5061.6951
1.26-1.31.066139920.61.3271
1.3-1.340.844136720.6951.0541
1.34-1.390.718130550.710.9061
1.39-1.440.579127980.8040.721
1.44-1.50.442123370.8670.5491
1.5-1.560.305118850.9290.381
1.56-1.640.215111790.9580.271
1.64-1.730.16107380.980.1991
1.73-1.830.111102210.9870.1391
1.83-1.960.0796630.9940.0881
1.96-2.120.04587030.9970.0571
2.12-2.320.03583170.9980.0441
2.32-2.590.02973750.9980.0371
2.59-30.02563520.9980.0311
3-3.670.01954520.9990.0241
3.67-5.190.01742330.9990.0221

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→42.7 Å / SU ML: 0.2077 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8068
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 2098 1.98 %
Rwork0.1758 103964 -
obs0.1762 106062 95.04 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 1.15→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 17 327 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792302
X-RAY DIFFRACTIONf_angle_d0.95613123
X-RAY DIFFRACTIONf_chiral_restr0.0798382
X-RAY DIFFRACTIONf_plane_restr0.0097404
X-RAY DIFFRACTIONf_dihedral_angle_d5.7032324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.180.57151000.59684950X-RAY DIFFRACTION68.22
1.18-1.210.4921170.52765798X-RAY DIFFRACTION80.27
1.21-1.240.46141350.41746700X-RAY DIFFRACTION92.67
1.24-1.270.3751430.32317066X-RAY DIFFRACTION97.51
1.27-1.320.32361440.27297133X-RAY DIFFRACTION98.07
1.32-1.360.3071440.25177121X-RAY DIFFRACTION98.26
1.36-1.420.26881440.22867169X-RAY DIFFRACTION98.54
1.42-1.480.24321450.20977183X-RAY DIFFRACTION98.77
1.48-1.560.19951460.15097189X-RAY DIFFRACTION99
1.56-1.660.1771440.13677176X-RAY DIFFRACTION98.63
1.66-1.790.16141470.13387274X-RAY DIFFRACTION99.25
1.79-1.970.17081470.13177262X-RAY DIFFRACTION99.44
1.97-2.250.14841460.13257251X-RAY DIFFRACTION99.21
2.25-2.830.17911470.15867305X-RAY DIFFRACTION99.12
2.83-42.70.18161490.17567387X-RAY DIFFRACTION98.32

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