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- PDB-6hvm: Structural characterization of CdaA-APO -

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Basic information

Entry
Database: PDB / ID: 6hvm
TitleStructural characterization of CdaA-APO
ComponentsDiadenylate cyclase
KeywordsTRANSFERASE / di-adenylate cyclase / second messenger / complex / c-di-AMP / AMP
Function / homology
Function and homology information


diadenylate cyclase activity / diadenylate cyclase / : / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane
Similarity search - Function
YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / 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. ...YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHeidemann, J.L. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structures of the c-di-AMP-synthesizing enzyme CdaA.
Authors: Heidemann, J.L. / Neumann, P. / Dickmanns, A. / Ficner, R.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)39,1164
Polymers38,7382
Non-polymers3782
Water2,054114
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4052
Polymers19,3691
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7112
Polymers19,3691
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.486, 64.896, 129.809
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 serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: dacA, cdaA, lmo2120 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y5E4, diadenylate cyclase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.7 M NaCl, 0.1 M Na-HEPES

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→45.891 Å / Num. obs: 24970 / % possible obs: 99.7 % / Redundancy: 7.13 % / Biso Wilson estimate: 44.378 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.094 / Χ2: 1.02 / Net I/σ(I): 16.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.17.1661.1023.0133110.7721.1998.5
2.1-2.27.2180.8084.2827350.8670.87399.9
2.2-2.67.2650.4377.9273310.9550.47299.9
2.6-2.87.2210.23913.9222720.9810.25799.9
2.8-37.2950.16218.8816730.9920.17599.8
3-47.1380.06130.5243220.9980.06699.9
4-56.7270.03740.0215800.9980.0499.9
5-66.5010.03142.977170.9990.03499.9
6-76.7740.03145.733630.9990.033100
7-86.7250.02457.0721110.026100
8-96.3750.02260.8612810.024100
9-106.560.02361.888410.025100
10-205.6760.02355.332100.9990.026100
20-304.2170.03445.882310.03995.8
30-502.8890.02840.4290.9980.03781.8
45.891-501150

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 2→45.891 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.16
RfactorNum. reflection% reflection
Rfree0.2245 1243 5 %
Rwork0.1858 --
obs0.1878 24874 99.02 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 156.17 Å2 / Biso mean: 47.6029 Å2 / Biso min: 22.21 Å2
Refinement stepCycle: final / Resolution: 2→45.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 24 114 2610
Biso mean--85.86 49.89 -
Num. residues----322
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)
11.2511-0.6794-0.76763.02790.24252.6791-0.0655-0.1408-0.35620.20560.07970.3870.0058-0.2117-0.01960.32560.0036-0.00450.31310.0250.3032-25.8189-2.8236-4.671
27.3728-2.41641.40444.2504-2.61134.856-0.03920.15220.2031-0.1660.083-0.3594-0.18550.2989-0.00350.28790.00620.00730.2481-0.07070.296-12.34571.6829-10.8537
32.58340.362-1.55431.27240.80055.54560.02660.74540.2677-0.50190.09680.6719-0.1962-1.269-0.04380.38380.0146-0.07390.42230.09220.3383-26.51783.4271-23.5373
41.6654-0.68651.05734.28250.50093.0719-0.04520.08960.3291-0.17550.0822-0.3681-0.12280.1748-0.1340.2537-0.0061-0.02320.2845-0.03170.3198-15.3996-6.7825-15.3166
50.9192-0.0558-0.2217.09130.25791.891-0.28350.048-0.1216-0.68770.3043-0.5366-0.2074-0.0597-0.12530.27220.01290.0070.268-0.00950.176-16.66517.3726-19.6301
65.30150.73230.94994.94040.77964.4909-0.0191-0.28640.8149-0.7283-0.0597-0.3872-0.18910.0173-0.04240.4431-0.07280.05520.28170.04950.3058-15.691511.5588-19.9273
77.4752-0.8014.76935.2963-1.91817.3625-0.2750.13150.03850.01180.267-0.1809-0.50110.10490.09460.3239-0.01370.01410.2542-0.01390.2354-15.50518.6612-12.1441
83.80492.418-1.80822.5867-0.10883.26420.3409-0.14430.08150.4043-0.03750.0821-0.08720.1181-0.27120.43240.04820.0260.3266-0.03090.356-20.753811.7787-5.1563
93.69873.3136-1.79482.9742-1.60450.85180.5850.37960.335-0.3651-0.0340.9618-0.5001-0.0366-0.59330.69270.0678-0.08570.6982-0.10780.7087-41.406-0.4607-4.656
108.69680.22743.58173.91560.62685.40270.59870.5194-0.4603-0.738-0.13510.02020.3154-0.1987-0.26680.3861-0.02020.02390.34040.01120.31-15.7342-22.321-25.9497
110.3180.02620.8974.21340.23494.1877-0.1838-0.6319-0.30070.06150.04340.53880.0163-0.70150.20040.2260.00490.01160.40980.04320.3396-19.844-28.2313-12.5013
124.22330.67460.13333.29440.61712.0810.0726-0.2441-0.3810.04440.0708-0.2794-0.0056-0.1993-0.16730.2426-0.0151-0.00360.26550.03090.3448-15.4619-16.0142-12.4713
136.67090.49120.94278.06310.94222.0628-0.25190.3091-0.0165-0.89480.0280.8545-0.348-0.59250.11370.3229-0.0034-0.02660.36640.01560.2737-23.6833-21.1775-15.9096
141.8877-0.54720.12614.2944-0.75011.6818-0.131-0.1871-0.15860.36520.2405-0.48390.02410.2161-0.10120.3453-0.0298-0.06150.37810.01160.288-11.7225-33.6197-6.4569
158.10742.1978-1.76464.283-1.16512.2463-0.3576-0.29460.1186-0.13260.163-0.15380.14020.03590.11950.258-0.0195-0.03090.27770.00060.2875-10.6955-30.6263-15.1566
160.9388-1.69640.92213.3554-1.20817.49360.00070.3791-0.212-0.32580.2032-0.1370.58820.5472-0.20750.3209-0.0201-0.00560.3371-0.03490.4249-8.1416-36.9332-17.4634
176.77350.90514.84761.68161.67196.6755-0.10571.4055-0.2258-0.36330.2629-0.28730.2303-0.0936-0.35140.512-0.09020.02780.37910.00470.2832-15.8011-32.7458-27.923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 25 )A0 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 34 )A26 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 46 )A35 - 46
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 73 )A47 - 73
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 101 )A74 - 101
6X-RAY DIFFRACTION6chain 'A' and (resid 102 through 113 )A102 - 113
7X-RAY DIFFRACTION7chain 'A' and (resid 114 through 132 )A114 - 132
8X-RAY DIFFRACTION8chain 'A' and (resid 133 through 153 )A133 - 153
9X-RAY DIFFRACTION9chain 'A' and (resid 154 through 166 )A154 - 166
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 26 )B3 - 26
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 44 )B27 - 44
12X-RAY DIFFRACTION12chain 'B' and (resid 45 through 73 )B45 - 73
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 83 )B74 - 83
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 113 )B84 - 113
15X-RAY DIFFRACTION15chain 'B' and (resid 114 through 132 )B114 - 132
16X-RAY DIFFRACTION16chain 'B' and (resid 133 through 141 )B133 - 141
17X-RAY DIFFRACTION17chain 'B' and (resid 142 through 157 )B142 - 157

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