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- PDB-8s46: CdaA-E01 complex -

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Basic information

Entry
Database: PDB / ID: 8s46
TitleCdaA-E01 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
2-chlorobenzyl carbamimidothioate / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 Å
AuthorsNeumann, P. / Ficner, R.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
German Research Foundation (DFG)INST186/1117 Germany
German Research Foundation (DFG)SFB860 Germany
CitationJournal: To Be Published
Title: CdaA-E01 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)38,9624
Polymers38,7382
Non-polymers2242
Water1,09961
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3922
Polymers19,3691
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5702
Polymers19,3691
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.790, 64.650, 130.020
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 coli (E. coli) / References: UniProt: Q8Y5E4, diadenylate cyclase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-F06 / 2-chlorobenzyl carbamimidothioate


Mass: 200.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9ClN2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
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 PILATUS3 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: 1.99→45.84 Å / Num. obs: 44332 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.086 / Net I/σ(I): 11.58
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.99-2.092.58960790.4012.9331
2.09-2.191.53649640.6121.7421
2.19-2.390.79177060.8640.8991
2.39-80.053249210.9990.0611
8-140.01554010.0171
14-170.0136010.0151
17-500.019620.9990.0231

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.99→45.84 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.23 / Phase error: 36.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2219 5.01 %
Rwork0.2247 --
obs0.2264 44268 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 13 61 2418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022386
X-RAY DIFFRACTIONf_angle_d0.4933223
X-RAY DIFFRACTIONf_dihedral_angle_d12.428905
X-RAY DIFFRACTIONf_chiral_restr0.047390
X-RAY DIFFRACTIONf_plane_restr0.011417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.030.49411460.47472580X-RAY DIFFRACTION100
2.03-2.080.44561400.45292650X-RAY DIFFRACTION100
2.08-2.130.44281330.42462622X-RAY DIFFRACTION100
2.13-2.190.44611410.38052635X-RAY DIFFRACTION100
2.19-2.250.29921360.34122620X-RAY DIFFRACTION100
2.25-2.330.31931440.31972675X-RAY DIFFRACTION100
2.33-2.410.3121360.29392593X-RAY DIFFRACTION100
2.41-2.510.33331400.28752677X-RAY DIFFRACTION100
2.51-2.620.391400.28952610X-RAY DIFFRACTION100
2.62-2.760.28831390.24372629X-RAY DIFFRACTION100
2.76-2.930.27631320.2552642X-RAY DIFFRACTION100
2.93-3.160.26951350.2272597X-RAY DIFFRACTION98
3.16-3.480.23911350.20682630X-RAY DIFFRACTION100
3.48-3.980.20391420.17292665X-RAY DIFFRACTION100
3.98-5.010.18181460.1532614X-RAY DIFFRACTION100
5.01-45.840.22851340.18942610X-RAY DIFFRACTION99
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)
17.01920.842-1.93984.9439-0.9923.21130.6438-0.21280.30091.3015-0.433-0.1373-0.06530.1732-0.15130.9667-0.0832-0.0330.4360.01790.3999-22.646-0.699-4.173
22.81971.0787-0.80787.8021-0.03865.72710.21380.1063-0.2093-0.1468-0.07680.0615-0.0092-0.2911-0.02770.4166-0.002-0.01080.3186-0.00280.3298-20.848-1.311-16.525
34.6456-2.37581.14866.56650.27124.105-0.2010.242-0.2033-0.0712-0.026-0.4616-0.38430.13750.1190.5036-0.0077-0.06870.30620.01060.3959-17.559-3.748-17.57
43.89790.9661-0.13022.55121.40980.95230.21530.4510.1615-1.09670.17340.1492-0.96940.5161-0.20380.8508-0.03690.04560.4131-0.00450.3172-16.3558.716-24.669
51.12310.3658-0.2526.6284-0.85183.1530.3778-0.10110.19370.0294-0.2806-0.5308-0.29130.27390.00240.7148-0.04210.01390.4127-0.0320.4186-14.48612.189-15.965
61.90450.90310.67733.5162-3.93256.14750.6720.06980.50591.0348-0.15480.2766-2.07890.2619-0.15540.9787-0.07350.09270.5228-0.10880.517-16.55515.877-9.282
79.21232.06423.07144.14210.03145.65020.341-0.80340.36430.3286-0.3468-0.1636-0.2461-0.19340.12781.0416-0.05910.0490.48-0.03170.5257-25.2659.503-2.723
83.6142-0.8505-0.01666.1576-0.39275.8152-0.09420.05220.0746-0.1858-0.1053-0.21840.1919-0.13470.18230.502-0.04440.01660.32080.00210.4025-18.007-20.468-17.415
93.137-3.01262.77928.107-0.70356.3318-0.0358-0.08570.21511.10980.2397-0.65820.29620.322-0.13910.6983-0.035-0.11210.42880.00690.4912-12.348-33.221-6.992
107.858-0.0278-0.96685.4259-0.75156.14620.07250.1436-0.7123-0.29890.0097-0.79830.67560.2267-0.07260.56340.0375-0.01540.35790.05590.4305-11.458-30.198-15.791
116.4503-2.41722.61645.3539-3.75568.42080.72340.4930.0497-0.814-0.36-0.05350.9057-0.0703-0.29710.76870.01520.05830.4004-0.0170.4756-14.332-34.07-24.489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:25 )A5 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:62 )A26 - 62
3X-RAY DIFFRACTION3( CHAIN A AND RESID 63:83 )A63 - 83
4X-RAY DIFFRACTION4( CHAIN A AND RESID 84:93 )A84 - 93
5X-RAY DIFFRACTION5( CHAIN A AND RESID 94:132 )A94 - 132
6X-RAY DIFFRACTION6( CHAIN A AND RESID 133:141 )A133 - 141
7X-RAY DIFFRACTION7( CHAIN A AND RESID 142:155 )A142 - 155
8X-RAY DIFFRACTION8( CHAIN B AND RESID 5:83 )B5 - 83
9X-RAY DIFFRACTION9( CHAIN B AND RESID 84:113 )B84 - 113
10X-RAY DIFFRACTION10( CHAIN B AND RESID 114:132 )B114 - 132
11X-RAY DIFFRACTION11( CHAIN B AND RESID 133:156 )B133 - 156

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