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- PDB-8s45: CdaA-E05 complex -

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Basic information

Entry
Database: PDB / ID: 8s45
TitleCdaA-E05 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
: / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 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-E05 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)38,9923
Polymers38,7382
Non-polymers2531
Water3,081171
1
A: Diadenylate cyclase


Theoretical massNumber of molelcules
Total (without water)19,3691
Polymers19,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6222
Polymers19,3691
Non-polymers2531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.750, 64.710, 129.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-G3Y / (1~{R},2~{S},3~{S},4~{R},5~{S})-2-azanyl-4-phenylsulfanyl-6,8-dioxabicyclo[3.2.1]octan-3-ol


Mass: 253.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H15NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 0.9677 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: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.69→39.72 Å / Num. obs: 74891 / % possible obs: 99 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.057 / Net I/σ(I): 13.12
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.69-1.792.055118910.5212.351
1.79-1.891.14894920.7591.31
1.89-2.090.485140200.9330.5491
2.09-80.036387920.9990.0411
8-140.0185730.9980.0221
14-170.0225710.0271
17-500.0176610.021

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.69→39.72 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.19 / Phase error: 33.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 3748 5.01 %
Rwork0.1964 71061 -
obs0.1983 74809 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.95 Å2 / Biso mean: 43.1154 Å2 / Biso min: 25.66 Å2
Refinement stepCycle: final / Resolution: 1.69→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 17 171 2573
Biso mean--41.5 45.74 -
Num. residues----310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.710.63581370.55522571270897
1.71-1.730.50261410.53352641278299
1.73-1.760.53471400.48462655279599
1.76-1.780.50941350.42872643277899
1.78-1.810.44351420.40652655279799
1.81-1.840.36611390.36232628276799
1.84-1.870.36731380.33112618275699
1.87-1.90.38331400.31862665280599
1.9-1.930.29191360.28652630276699
1.93-1.970.30711390.26452664280399
1.97-2.010.26221400.25012654279499
2.01-2.060.31941380.2412604274299
2.06-2.10.24181370.23462647278499
2.1-2.160.26541460.20712651279799
2.16-2.210.26881340.19412592272699
2.21-2.280.22341390.19422641278099
2.28-2.350.25371400.19812627276799
2.35-2.440.25421370.18792615275298
2.44-2.530.20881360.19072610274699
2.53-2.650.29021400.19882673281399
2.65-2.790.25821410.20282648278999
2.79-2.960.20211360.19622567270397
2.96-3.190.26641370.18552577271496
3.19-3.510.18551410.164926442785100
3.52-4.020.16021390.145426542793100
4.02-5.070.15331410.136326532794100
5.07-39.720.2561390.18542634277399
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)
16.48281.0505-2.05563.93230.56353.09640.5599-0.19920.2280.6546-0.39880.3150.1187-0.4965-0.08970.6032-0.08750.0270.3834-0.01450.2556-27.1424-1.3508-4.8206
21.01470.8551-0.15925.47490.24532.4996-0.04880.01240.0137-0.05470.1459-0.1759-0.2714-0.0865-0.06010.22960.00560.01340.1961-0.00990.1667-19.60233.0393-17.8917
32.10980.97312.16745.4333-1.56276.1801-0.00740.00130.27160.3441-0.0068-0.4562-1.17610.10950.01080.4924-0.0277-0.02070.3498-0.04370.3299-15.505112.0378-9.7152
48.91661.86253.69026.85051.41266.60480.3791-0.70510.69360.6714-0.38340.3326-0.6112-0.86740.00340.5435-0.00640.08370.39290.00490.3223-26.80889.0926-2.9899
55.5805-1.18651.6882.6379-0.84655.7655-0.00320.4273-0.0227-0.5082-0.03-0.07950.1839-0.15-0.05280.4524-0.02570.05220.25650.00020.2933-17.581-24.2798-25.3547
60.5363-1.40050.32075.4725-0.91462.2915-0.0506-0.1513-0.02080.49030.1257-0.14020.0132-0.2008-0.05320.3626-0.0466-0.02830.29920.00370.2828-19.2395-23.552-11.245
73.2707-0.4259-1.5373.9521-0.91474.16140.0713-0.0658-0.08190.13780.0147-0.26480.4470.0809-0.0470.4071-0.0239-0.02950.25010.00580.2686-14.2169-32.9282-17.4696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 121 )A26 - 121
3X-RAY DIFFRACTION3chain 'A' and (resid 122 through 141 )A122 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 155 )A142 - 155
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 34 )B0 - 34
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 101 )B35 - 101
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 154 )B102 - 154

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