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- PDB-8s4a: CdaA-B04 complex -

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Basic information

Entry
Database: PDB / ID: 8s4a
TitleCdaA-B04 complex
ComponentsDiadenylate cyclase
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


diadenylate cyclase activity / diadenylate cyclase / 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
: / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.23 Å
AuthorsNeumann, P. / Ficner, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
German Research Foundation (DFG)SFB860 Germany
CitationJournal: To Be Published
Title: CdaA-B04 complex
Authors: Neumann, P. / Ficner, R.
History
DepositionFeb 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / chem_comp_bond ...chem_comp / chem_comp_bond / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp_bond.atom_id_1 ..._chem_comp.name / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)39,2105
Polymers38,7382
Non-polymers4723
Water2,162120
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5872
Polymers19,3691
Non-polymers2181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6233
Polymers19,3691
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.700, 64.460, 128.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 phage EcSzw-2 (virus) / References: UniProt: Q8Y5E4, diadenylate cyclase
#2: Chemical ChemComp-AJO / 2-[cyanomethyl(methyl)amino]-N-(6-methylpyridin-2-yl)ethanamide


Mass: 218.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.23→45.54 Å / Num. obs: 31425 / % possible obs: 96.1 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.149 / Net I/σ(I): 8.04
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.23-2.331.48638970.371.7411
2.33-2.431.20832240.4791.4131
2.43-2.630.88351060.5931.0331
2.63-80.102184990.9950.1161
8-140.0335790.9970.0371
14-170.031560.9990.0361
17-500.035640.9990.0411

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.23→45.54 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 1572 5.01 %
Rwork0.2008 --
obs0.2031 31404 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 33 120 2485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032394
X-RAY DIFFRACTIONf_angle_d0.5343233
X-RAY DIFFRACTIONf_dihedral_angle_d11.856913
X-RAY DIFFRACTIONf_chiral_restr0.049391
X-RAY DIFFRACTIONf_plane_restr0.004424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.30.3931420.33772743X-RAY DIFFRACTION96
2.3-2.380.38541450.33042689X-RAY DIFFRACTION96
2.38-2.480.30141410.29792707X-RAY DIFFRACTION95
2.48-2.590.32711440.28882689X-RAY DIFFRACTION96
2.59-2.730.33371350.27432654X-RAY DIFFRACTION94
2.73-2.90.36031220.25552308X-RAY DIFFRACTION82
2.9-3.120.25311480.19472778X-RAY DIFFRACTION98
3.12-3.440.24941430.18322819X-RAY DIFFRACTION100
3.44-3.940.19821500.152801X-RAY DIFFRACTION100
3.94-4.960.19551530.14322832X-RAY DIFFRACTION100
4.96-45.540.18911490.18662812X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.37611.0148-2.13653.16720.45262.7860.1191-0.147-0.23170.5252-0.15060.030.0908-0.2401-0.01880.5224-0.0348-0.02940.45450.00630.3272-21.4036-0.936-4.2026
21.53070.46660.78385.84230.01283.3155-0.17840.02960.1124-0.150.1307-0.1529-0.2473-0.0670.03930.21770.0043-0.00840.2153-0.01320.1612-15.9713.4478-16.9412
32.69941.7083-2.3491.7932-0.1364.78590.068-0.3203-0.01180.8896-0.00470.3631-0.6173-0.10550.10220.5966-0.01230.00720.3197-0.02980.4148-20.562911.4938-5.1615
48.11320.09014.03014.1707-0.15027.5141-0.18850.52490.0596-0.47210.30820.2585-0.2887-0.0878-0.0930.41630.01750.01570.32660.05930.3801-14.9623-22.2761-25.7901
54.048-1.38850.22643.7031-0.1784.8108-0.0505-0.5755-0.0934-0.02330.15160.30340.1864-0.4825-0.09090.3442-0.0425-0.09570.26820.00170.2805-17.4942-26.3515-13.086
65.39-2.05282.46136.1578-0.07131.2484-0.2453-0.36790.35961.14180.12490.37960.1861-0.6029-0.27320.17-0.10780.06180.26030.00330.1556-22.05-16.7109-12.3768
73.58160.4749-2.03686.8448-0.09323.19010.0106-0.28940.0840.0855-0.0234-0.3070.0602-0.2074-0.0520.2578-0.0855-0.01270.28680.01290.31-14.8584-17.4301-13.6627
81.5838-0.4999-0.02315.6168-0.2832.8314-0.0323-0.3521-0.10160.66810.2707-0.15660.2476-0.1621-0.09370.4603-0.0648-0.05640.29460.01650.2928-11.8503-33.1934-8.5642
95.05160.918-1.88224.5812-1.3774.2763-0.4194-0.2607-0.2120.83420.4478-0.84110.26930.64820.00620.4664-0.0035-0.11440.3793-0.04240.3403-5.4088-30.0315-15.411
101.1214-1.5102-0.39512.3647-0.61765.74740.0124-0.1884-0.42670.2608-0.0184-1.05911.0650.4178-0.19990.62310.0832-0.17170.4176-0.07460.4901-7.5898-36.8999-17.8954
115.5859-0.8806-1.09413.977-0.77626.65120.38020.5591-0.6130.03550.0590.40850.1351-0.6366-0.33990.5667-0.0061-0.00730.33030.00430.3126-15.3954-32.9608-27.8273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 155 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 44 )
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 55 )
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 83 )
8X-RAY DIFFRACTION8chain 'B' and (resid 84 through 121 )
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 132 )
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 141 )
11X-RAY DIFFRACTION11chain 'B' and (resid 142 through 157 )

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