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- PDB-8c4m: CdaA-Adenosine complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8c4m
TitleCdaA-Adenosine 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 / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.51 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)39,1126
Polymers38,7382
Non-polymers3744
Water4,071226
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6723
Polymers19,3691
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4403
Polymers19,3691
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.140, 64.520, 129.550
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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
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: P14 (MX2) / Wavelength: 0.97702 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 56384 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 27.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.053 / Net I/σ(I): 20.41
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.51-1.573.98656250.6624.1411
1.57-1.622.6649020.7872.7631
1.62-1.731.7380400.8761.7981
1.73-80.0433735610.0441
8-140.0236410.0211
14-170.028390.9980.031
17-500.0255810.0271

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.51→45.71 Å / SU ML: 0.2214 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.3612
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2493 2815 5 %
Rwork0.2059 53432 -
obs0.208 56247 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.05 Å2
Refinement stepCycle: LAST / Resolution: 1.51→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 22 226 2697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00442554
X-RAY DIFFRACTIONf_angle_d0.65593461
X-RAY DIFFRACTIONf_chiral_restr0.0525417
X-RAY DIFFRACTIONf_plane_restr0.0057441
X-RAY DIFFRACTIONf_dihedral_angle_d12.9145963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.540.57011390.52542607X-RAY DIFFRACTION99.49
1.54-1.560.53791380.49292636X-RAY DIFFRACTION99.64
1.56-1.590.48031350.44242578X-RAY DIFFRACTION99.38
1.59-1.630.4361390.40022668X-RAY DIFFRACTION99.79
1.63-1.660.42721390.36542628X-RAY DIFFRACTION99.71
1.66-1.70.44081390.35342637X-RAY DIFFRACTION99.86
1.7-1.740.41091400.33712653X-RAY DIFFRACTION99.82
1.74-1.790.37081380.30832635X-RAY DIFFRACTION99.78
1.79-1.840.32631400.2912651X-RAY DIFFRACTION99.89
1.84-1.90.30481400.25732658X-RAY DIFFRACTION100
1.9-1.970.29461390.2152638X-RAY DIFFRACTION99.93
1.97-2.050.25041390.19312642X-RAY DIFFRACTION99.93
2.05-2.140.25421410.19972683X-RAY DIFFRACTION99.86
2.14-2.260.25341410.20132669X-RAY DIFFRACTION99.86
2.26-2.40.22521420.18362683X-RAY DIFFRACTION99.93
2.4-2.580.26081420.19172697X-RAY DIFFRACTION100
2.58-2.840.23331420.20282708X-RAY DIFFRACTION100
2.84-3.250.26861440.1932718X-RAY DIFFRACTION99.93
3.25-4.10.20311450.1652749X-RAY DIFFRACTION100
4.1-45.710.20231530.18462894X-RAY DIFFRACTION99.87

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