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- PDB-8c4r: CdaA-adenine complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8c4r
TitleCdaA-adenine 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
ADENINE / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 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)39,0157
Polymers38,7382
Non-polymers2775
Water3,981221
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5754
Polymers19,3691
Non-polymers2063
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)42.740, 64.580, 129.650
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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
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: Oct 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 53052 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 31.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.053 / Net I/σ(I): 20.21
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.55-1.613.60851830.7113.7331
1.61-1.662.66245120.812.7531
1.66-1.771.63174740.9121.6871
1.77-80.0463541910.0471
8-140.0253700.9990.0261
14-170.0243810.0261
17-500.029560.9990.0321

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→40.59 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.3991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 2644 5 %
Rwork0.197 50242 -
obs0.199 52886 99.78 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.68 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 14 221 2601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01262441
X-RAY DIFFRACTIONf_angle_d1.13693303
X-RAY DIFFRACTIONf_chiral_restr0.0787397
X-RAY DIFFRACTIONf_plane_restr0.011422
X-RAY DIFFRACTIONf_dihedral_angle_d15.0893922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.51311370.50142605X-RAY DIFFRACTION99.13
1.58-1.610.45311330.44762543X-RAY DIFFRACTION99.04
1.61-1.640.46161380.42512633X-RAY DIFFRACTION99.5
1.64-1.680.46051360.3972593X-RAY DIFFRACTION99.85
1.68-1.720.40011370.36362620X-RAY DIFFRACTION99.78
1.72-1.760.35751360.32232599X-RAY DIFFRACTION99.74
1.76-1.810.32041390.2822629X-RAY DIFFRACTION99.75
1.81-1.860.34161380.2452615X-RAY DIFFRACTION99.93
1.86-1.920.25071380.2142613X-RAY DIFFRACTION99.93
1.92-1.990.24971380.22042637X-RAY DIFFRACTION99.93
1.99-2.070.27631390.2112623X-RAY DIFFRACTION99.89
2.07-2.160.24731390.17362638X-RAY DIFFRACTION99.82
2.16-2.280.19341400.16532652X-RAY DIFFRACTION99.86
2.28-2.420.26621390.17732629X-RAY DIFFRACTION99.93
2.42-2.610.20941400.19662667X-RAY DIFFRACTION100
2.61-2.870.24631410.21032676X-RAY DIFFRACTION99.96
2.87-3.280.23181420.1922692X-RAY DIFFRACTION99.93
3.28-4.130.18421430.16292721X-RAY DIFFRACTION100
4.14-40.590.22281510.18232857X-RAY DIFFRACTION99.73

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