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

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Basic information

Entry
Database: PDB / ID: 8ohg
TitlePanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry F09
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: 1.25 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 F09
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)33,5584
Polymers33,3622
Non-polymers1962
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-13 kcal/mol
Surface area14160 Å2
Unit cell
Length a, b, c (Å)118.890, 39.200, 68.160
Angle α, β, γ (deg.)90.000, 95.360, 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-449-

HOH

21B-471-

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-UI4 / 4-pyridin-2-ylphenol


Mass: 171.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9NO / 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.: 155 / 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: 48.1 %
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: 1.25→50 Å / Num. obs: 153137 / % possible obs: 94.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 17.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.064 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.27-1.31.741112810.2632.1691
1.3-1.341.463109360.3161.8231
1.34-1.381.233104640.3591.541
1.38-1.420.979104170.4681.2161
1.42-1.470.771101970.5930.9561
1.47-1.520.57498540.710.7121
1.52-1.580.40595430.8390.5021
1.58-1.640.29688620.9020.3681
1.64-1.710.23888230.9450.2931
1.71-1.80.17484180.9640.2151
1.8-1.890.12380980.9810.1511
1.89-2.010.08175410.9920.11
2.01-2.150.05968860.9950.0731
2.15-2.320.04766970.9970.0571
2.32-2.540.0460920.9970.0491
2.54-2.840.03454710.9980.0421
2.84-3.280.02646230.9980.0331
3.28-4.020.02141020.9990.0251
4.02-5.680.0230950.9990.0251

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→32.23 Å / SU ML: 0.1789 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2032 2100 2.53 %
Rwork0.1816 80999 -
obs0.1822 83099 95.51 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.14 Å2
Refinement stepCycle: LAST / Resolution: 1.25→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 14 155 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422335
X-RAY DIFFRACTIONf_angle_d0.77173169
X-RAY DIFFRACTIONf_chiral_restr0.0669384
X-RAY DIFFRACTIONf_plane_restr0.0062410
X-RAY DIFFRACTIONf_dihedral_angle_d6.5128328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.44671320.44695101X-RAY DIFFRACTION91.29
1.28-1.310.42491380.38615293X-RAY DIFFRACTION93.61
1.31-1.350.38041370.3555270X-RAY DIFFRACTION94.36
1.35-1.390.34691360.32465274X-RAY DIFFRACTION93.74
1.39-1.430.33131390.30035336X-RAY DIFFRACTION95.15
1.43-1.480.26981390.25375360X-RAY DIFFRACTION95.27
1.48-1.540.24931390.20645391X-RAY DIFFRACTION95.84
1.54-1.610.21521410.17965427X-RAY DIFFRACTION95.87
1.61-1.70.18861390.15795379X-RAY DIFFRACTION95.43
1.7-1.80.18011410.15325444X-RAY DIFFRACTION96.46
1.8-1.940.22131420.14935482X-RAY DIFFRACTION97.13
1.94-2.140.17351410.14855422X-RAY DIFFRACTION95.9
2.14-2.440.19351440.15275579X-RAY DIFFRACTION98.03
2.44-3.080.21521430.17655517X-RAY DIFFRACTION96.6
3.08-32.230.16421490.17315724X-RAY DIFFRACTION97.72

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