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- PDB-8s47: CdaA-D07 complex -

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Basic information

Entry
Database: PDB / ID: 8s47
TitleCdaA-D07 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
Chem-47U / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.11 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-D07 complex
Authors: Neumann, P. / Ficner, R.
History
DepositionFeb 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 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: Diadenylate cyclase
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2986
Polymers38,7382
Non-polymers5594
Water1,63991
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6493
Polymers19,3691
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6493
Polymers19,3691
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.220, 65.070, 130.330
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-47U / N-(pyridin-2-yl)-2-(1,3,5-trimethyl-1H-pyrazol-4-yl)acetamide


Mass: 244.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 91 / 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2018
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.11→46.04 Å / Num. obs: 41718 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.117 / Net I/σ(I): 10.08
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.11-2.212.65153940.52.8611
2.21-2.311.57645220.7131.6991
2.31-2.510.96869820.8831.0441
2.51-80.086240590.9980.0921
8-140.0396250.9990.0411
14-170.039620.9990.0421
17-500.041740.9990.0441

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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: 2.11→46.04 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 2083 5 %
Rwork0.2059 --
obs0.2077 41687 99.76 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 38 91 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022435
X-RAY DIFFRACTIONf_angle_d0.417
X-RAY DIFFRACTIONf_dihedral_angle_d12.022935
X-RAY DIFFRACTIONf_chiral_restr0.045394
X-RAY DIFFRACTIONf_plane_restr0.003447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.160.51951390.41972597X-RAY DIFFRACTION99
2.16-2.210.42931420.37012672X-RAY DIFFRACTION100
2.21-2.270.3641350.32762600X-RAY DIFFRACTION100
2.27-2.340.33531420.34472681X-RAY DIFFRACTION100
2.34-2.420.32681430.31572616X-RAY DIFFRACTION99
2.42-2.50.33291390.28232645X-RAY DIFFRACTION100
2.5-2.60.32271440.27022653X-RAY DIFFRACTION100
2.6-2.720.30121360.25522620X-RAY DIFFRACTION100
2.72-2.860.33481360.24282632X-RAY DIFFRACTION100
2.86-3.040.34221380.24432663X-RAY DIFFRACTION100
3.04-3.280.28181360.21162655X-RAY DIFFRACTION100
3.28-3.610.2381340.18762638X-RAY DIFFRACTION100
3.61-4.130.21451380.1582646X-RAY DIFFRACTION100
4.13-5.20.13881330.14212642X-RAY DIFFRACTION100
5.2-46.040.18641480.17882644X-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)
13.5763-1.14990.21556.3202-0.06293.21040.2406-0.6494-0.79750.59770.00120.31860.24-0.3852-0.1870.7496-0.0607-0.00430.59010.05370.4759-24.1671-1.4524-4.4546
21.6196-1.11810.07227.3304-0.28864.89980.00570.1149-0.0667-0.33680.1037-0.1793-0.0244-0.3149-0.13040.4696-0.0301-0.00070.4096-0.00390.4015-20.1961-2.6234-17.1037
34.13853.3396-0.63933.7474-2.1592.6026-0.62070.6129-0.4547-2.16680.7045-1.2976-0.5870.1014-0.03750.7502-0.0860.08260.4375-0.00140.5439-12.687312.872-21.0432
43.2581.7986-1.50595.6934-1.19294.74960.0408-0.04840.3578-0.08840.03470.0029-0.6738-0.0091-0.06130.646-0.00370.01070.3569-0.04640.3996-19.313410.6237-10.7876
59.6384-3.5480.87249.4242-0.87166.00840.37341.0492-0.1155-1.18230.0030.34540.2228-0.0888-0.29120.6968-0.04160.04130.44610.05810.4004-15.7094-22.212-25.7661
62.8006-1.02730.47548.7338-0.96635.99170.0808-0.2484-0.69580.11020.25880.4210.1502-0.7534-0.2540.5114-0.0269-0.06390.46270.08750.4732-20.7628-27.289-12.7507
75.025-2.83551.62777.1299-0.08432.2311-0.1935-0.26970.2480.38950.39320.25740.0207-0.7539-0.08170.4815-0.0842-0.0310.48080.02810.62-23.986-16.7877-12.8112
83.49160.5216-1.30987.48930.17262.0344-0.03-0.417-0.14130.65720.1492-1.17990.4120.0609-0.09650.5345-0.0132-0.1220.4375-0.02130.6098-12.2822-15.692-12.506
96.6805-3.20161.53695.3111-0.83985.1062-0.4356-0.3143-0.1840.61210.38770.5340.1798-0.42690.02420.5171-0.0616-0.07480.41010.03370.4246-20.7369-25.5921-10.1767
102.33792.5844-4.60072.0015-5.73299.15710.1129-1.5055-0.253-0.3025-1.1817-2.22741.32411.91250.23410.4566-0.045-0.21590.68460.03390.7128-4.8314-38.5343-6.9511
114.4867-0.9703-0.58496.7228-0.88616.0904-0.1479-0.3214-0.23140.37930.2161-0.26110.45180.1506-0.0960.5634-0.0124-0.0630.4133-0.00450.4744-12.0045-33.122-13.5703
123.5741-3.1687-1.36074.4595-2.46038.6452-0.22550.8464-0.7456-1.28260.09250.29170.9284-0.26350.01190.8414-0.039-0.04970.4976-0.02490.4468-16.8909-33.1456-27.9485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 155 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 26 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 44 )
7X-RAY DIFFRACTION7chain 'B' and (resid 45 through 55 )
8X-RAY DIFFRACTION8chain 'B' and (resid 56 through 73 )
9X-RAY DIFFRACTION9chain 'B' and (resid 74 through 93 )
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 102 through 141 )
12X-RAY DIFFRACTION12chain 'B' and (resid 142 through 157 )

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