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- PDB-8c4n: CdaA-AMP complex -

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Basic information

Entry
Database: PDB / ID: 8c4n
TitleCdaA-AMP complex
ComponentsDiadenylate cyclase
KeywordsPROTEIN BINDING / Complex
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
ADENOSINE MONOPHOSPHATE / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsNeumann, P. / Ficner, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
German Research Foundation (DFG)SFB860 Germany
CitationJournal: Microlife / Year: 2023
Title: Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor.
Authors: Neumann, P. / Kloskowski, P. / Ficner, R.
History
DepositionJan 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diadenylate cyclase
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5277
Polymers38,7382
Non-polymers7885
Water1,11762
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7393
Polymers19,3691
Non-polymers3702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7874
Polymers19,3691
Non-polymers4183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.610, 64.720, 129.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Diadenylate cyclase / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase / Diadenylate cyclase CdaA


Mass: 19369.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: dacA, cdaA, lmo2120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y5E4, diadenylate cyclase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.7 M NaCl, 0.1M Na-HEPES pH 8.5 and 3 % DMSO

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97702 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 68334 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 38.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.054 / Net I/σ(I): 14.13
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.75-1.82.89360240.5763.1251
1.8-1.861.96653540.7052.1331
1.86-1.971.21190420.8551.311
1.97-80.045471970.9990.0491
8-140.0285850.9990.0311
14-170.026600.9990.0291
17-500.033720.9980.0371

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→45.85 Å / SU ML: 0.2657 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 38.4753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2546 3422 5.02 %
Rwork0.2215 64787 -
obs0.2232 68209 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.78 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 49 62 2566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672556
X-RAY DIFFRACTIONf_angle_d0.89993463
X-RAY DIFFRACTIONf_chiral_restr0.0612415
X-RAY DIFFRACTIONf_plane_restr0.007432
X-RAY DIFFRACTIONf_dihedral_angle_d7.4532360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.53271410.51472633X-RAY DIFFRACTION99.53
1.78-1.80.52131440.49882764X-RAY DIFFRACTION99.73
1.8-1.830.44831370.46252633X-RAY DIFFRACTION99.86
1.83-1.860.48281460.45462727X-RAY DIFFRACTION99.79
1.86-1.890.44791450.42812713X-RAY DIFFRACTION99.69
1.89-1.930.45971420.41442668X-RAY DIFFRACTION99.93
1.93-1.960.37671440.37812731X-RAY DIFFRACTION99.83
1.96-20.34251370.34892673X-RAY DIFFRACTION99.68
2-2.050.32831390.2942713X-RAY DIFFRACTION99.86
2.05-2.090.34941430.27752738X-RAY DIFFRACTION99.93
2.09-2.150.34541410.25612676X-RAY DIFFRACTION100
2.15-2.20.30931470.24932727X-RAY DIFFRACTION99.69
2.2-2.270.2621400.23462664X-RAY DIFFRACTION99.64
2.27-2.340.28561410.24332721X-RAY DIFFRACTION99.72
2.34-2.430.281360.22662709X-RAY DIFFRACTION99.89
2.43-2.520.30041440.22892660X-RAY DIFFRACTION99.89
2.52-2.640.29561440.24482737X-RAY DIFFRACTION99.97
2.64-2.780.26741470.24622704X-RAY DIFFRACTION99.96
2.78-2.950.36571430.25312717X-RAY DIFFRACTION99.93
2.95-3.180.29121390.2282677X-RAY DIFFRACTION99.89
3.18-3.50.18941500.20752715X-RAY DIFFRACTION99.97
3.5-4.010.21491380.18382682X-RAY DIFFRACTION99.82
4.01-5.050.18391490.15862711X-RAY DIFFRACTION99.86
5.05-45.850.20991450.19142694X-RAY DIFFRACTION99.82

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