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- PDB-8c4o: CdaA-ATP complex -

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Basic information

Entry
Database: PDB / ID: 8c4o
TitleCdaA-ATP 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
ADENOSINE-5'-TRIPHOSPHATE / : / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.97 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)39,9779
Polymers38,7382
Non-polymers1,2397
Water82946
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9864
Polymers19,3691
Non-polymers6173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9915
Polymers19,3691
Non-polymers6224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.500, 64.650, 129.390
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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 53 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.29 Å3/Da / Density % sol: 46.39 %
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: P13 (MX1) / Wavelength: 0.97702 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 26034 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 46.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.115 / Net I/av σ(I): 12.78 / Net I/σ(I): 12.78
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.97-2.034.76720450.4484.9241
2.03-2.083.62617880.6393.7471
2.08-2.192.27431180.8322.351
2.19-80.103186150.9990.1071
8-140.0543680.9980.0561
14-170.052400.9980.0541
17-500.055600.9890.061

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.97→45.73 Å / SU ML: 0.2983 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.4599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2539 1299 5.01 %
Rwork0.2347 24634 -
obs0.2358 25933 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.18 Å2
Refinement stepCycle: LAST / Resolution: 1.97→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 67 46 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312441
X-RAY DIFFRACTIONf_angle_d1.10183316
X-RAY DIFFRACTIONf_chiral_restr0.0773397
X-RAY DIFFRACTIONf_plane_restr0.0109412
X-RAY DIFFRACTIONf_dihedral_angle_d15.2577904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.050.53921430.51882690X-RAY DIFFRACTION99.79
2.05-2.140.42331410.45492693X-RAY DIFFRACTION99.61
2.14-2.260.41531420.38672683X-RAY DIFFRACTION99.4
2.26-2.40.38341430.32972706X-RAY DIFFRACTION99.72
2.4-2.580.29521410.27532708X-RAY DIFFRACTION99.82
2.58-2.840.28171450.27132740X-RAY DIFFRACTION99.79
2.84-3.250.2821450.252736X-RAY DIFFRACTION99.72
3.25-4.10.23051450.19992760X-RAY DIFFRACTION99.73
4.1-45.730.19421540.1822918X-RAY DIFFRACTION99.71
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)
14.72710095649-0.10538518118-0.7999628404713.377435578980.07058445266063.21322760908-0.156936078285-0.499939497439-0.07499115662040.7417881518380.101681166013-0.02044626671660.0358099230166-0.45600590544-0.004432586577410.759495156675-0.0447806635741-0.1141681016050.6803166828570.02094593421830.601821279389-20.0000138509-0.0841523692101-6.02278732899
21.291114814410.7377360429530.6504861616965.546982107540.06621366523892.49008064367-0.05962848252680.1582529507260.0248346409163-0.4384758335530.142220854285-0.220788551135-0.307264000166-0.105008390463-0.04647467390590.580062132059-0.00983369792887-0.01199903661410.566511206613-0.004121238826070.457448990062-16.9129660974.03445098892-17.7029096185
32.937599863611.2606242239-1.684084013052.64349547743-0.6918725664674.13006216480.573761981334-0.1751105615980.2252309147420.321126848091-0.304315446096-0.0349506342701-0.7672966621340.0988051053406-0.1176121790670.8244582210570.0755691124388-0.0407516296980.607972667617-0.040684080680.628177862373-21.085245129511.6584617708-5.21839933633
46.86565573818-0.1875287870231.185663605523.723417986870.5578277649074.393915474090.1692502824361.216461012030.035641795657-0.605111029491-0.02415301764550.0681649173598-0.13146694112-0.1824530895690.1495935001640.6463021675220.002499416528650.0313374742740.6452593384780.02028880847060.596730766225-15.050043194-22.0271217809-26.1199653413
53.33353370083-0.1184830810461.115867934083.934228046260.2694894940993.52944589712-0.117864898221-0.4017754487290.1410464625780.4029385510480.1114970429420.01766660767360.138626363521-0.03335252631590.1235589302750.53847576367-9.64633689884E-5-0.1293795439220.5466236147920.01396782988270.554084009802-17.7437515573-26.1017208457-13.2491260707
67.39025240492-0.696566661633.286812018413.315210477990.4345657230093.40188360752-0.0349580835114-0.5135921738340.6022097320670.4120285726840.2686101778790.144300384786-0.294929213509-0.571764543637-0.0005692993756450.516600920883-0.06652523284080.07742048988580.562753503712-0.03805764430290.627646199704-22.3761459195-16.4769363875-12.5685705934
72.56591969705-0.4312574128530.1262532728814.80685074225-1.137272344462.89102111688-0.001219173300890.01556172243130.001194727041280.390509494650.154577366037-0.6592064168140.03138465824930.232081630885-0.09069695122270.426013688695-0.0486173482269-0.0569565200150.54386808052-0.01533708649480.59914450297-15.0624944317-17.1134551756-13.7943803267
80.239309712512-0.7484591297170.4307716327283.46778419331-0.4908205749811.921176721420.0924528120614-0.109632394011-0.1190801298280.609438937110.289321723269-0.4263949179580.2098902842030.243126033751-0.2261610015860.755609408732-0.0466059601082-0.150041477230.6459531515750.02046950432180.590477782751-10.8608821903-33.5589680478-6.79521738922
93.533078572640.208538919744-0.5770436632643.12036130083-0.8895666411174.371191703390.182781466372-0.475917978767-0.185443780353-0.335050813813-0.0135961559012-0.02983734876231.040532853610.152989887881-0.09935119144650.589165886854-0.0354191962551-0.1393143397130.6119021614350.0007850566647530.598567817572-9.67597395191-32.4292631692-16.25832163
104.47338543449-0.619235062150.06642871789295.11380578712-0.3196930027434.78546332330.06786544277460.800676484165-0.623345730055-0.5337867307140.02266356067630.418120768890.799004508026-0.480299045092-0.3191807733840.748095742108-0.0453139646224-0.1298746904320.579501403601-0.009905531827390.569511135447-14.7704092217-32.5127298766-27.6344625062
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 34 )AA4 - 341 - 31
22chain 'A' and (resid 35 through 132 )AA35 - 13232 - 129
33chain 'A' and (resid 133 through 155 )AA133 - 155130 - 152
44chain 'B' and (resid 5 through 25 )BB5 - 251 - 21
55chain 'B' and (resid 26 through 44 )BB26 - 4422 - 40
66chain 'B' and (resid 45 through 55 )BB45 - 5541 - 51
77chain 'B' and (resid 56 through 83 )BB56 - 8352 - 79
88chain 'B' and (resid 84 through 113 )BB84 - 11380 - 109
99chain 'B' and (resid 114 through 141 )BB114 - 141110 - 137
1010chain 'B' and (resid 142 through 155 )BB142 - 155138 - 151

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