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- PDB-6hvn: CdaA-APO Y187A Mutant -

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Basic information

Entry
Database: PDB / ID: 6hvn
TitleCdaA-APO Y187A Mutant
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: 2.234 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 / struct_asym / 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.pdbx_number_of_molecules / _entity.type / _struct_asym.entity_id
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)39,18011
Polymers38,5542
Non-polymers6269
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-91 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.490, 65.130, 131.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 5 and (name N or name...
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 5 and (name N or name...A5
121(chain A and ((resid 5 and (name N or name...A-4 - 170
131(chain A and ((resid 5 and (name N or name...A-4 - 170
141(chain A and ((resid 5 and (name N or name...A-4 - 170
151(chain A and ((resid 5 and (name N or name...A-4 - 170
211chain BB5 - 164

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Components

#1: Protein Diadenylate cyclase / / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase / Diadenylate cyclase CdaA


Mass: 19277.006 Da / Num. of mol.: 2 / Mutation: Y187A
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.: 8
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 4.0 M NaCl, 0.1 M Na-HEPES / PH range: 7.5-8.5

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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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.23→37.942 Å / Num. obs: 19512 / % possible obs: 97.1 % / Redundancy: 5.845 % / Biso Wilson estimate: 41.056 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.088 / Χ2: 0.984 / Net I/σ(I): 15.66 / Num. measured all: 114046
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.23-2.334.1570.522.87960241519150.8050.58679.3
2.33-2.435.4310.4444.0910954204320170.9120.4998.7
2.43-2.635.5420.3155.9117557319531680.9480.34899.2
2.63-86.290.06921.277484411911118980.9980.07599.9
8-145.4750.03339.8322234064060.9990.036100
14-175.3330.02941.1125648480.9990.032100
17-504.20.02533.41252636010.02895.2
37.942-504

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 2.234→37.942 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 974 5 %RANDOM
Rwork0.1837 18488 --
obs0.1859 19462 97.18 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.43 Å2 / Biso mean: 39.6268 Å2 / Biso min: 15.79 Å2
Refinement stepCycle: final / Resolution: 2.234→37.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 31 152 2725
Biso mean--74.14 44.58 -
Num. residues----334
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1448X-RAY DIFFRACTION16.668TORSIONAL
12B1448X-RAY DIFFRACTION16.668TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.234-2.35180.3011160.24522175229182
2.3518-2.49910.30011380.24432637277599
2.4991-2.6920.30241410.229326612802100
2.692-2.96280.2661410.206426922833100
2.9628-3.39130.27041420.193926942836100
3.3913-4.27180.18361450.147527512896100
4.2718-37.94770.17351510.163928783029100
Refinement TLS params.

S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.15760.0604-0.15530.85530.05580.57910.02160.0266-0.0417-0.0232-0.0128-0.0336-0.0529-0.04250.19160.0057-0.01070.20780.01020.1981-24.26912.8121-12.0882
20.3462-0.3459-0.13040.61910.09440.3880.0079-0.0460.0228-0.03370.022-0.00580.0048-0.03010.2021-0.0107-0.00710.19940.00850.2009-17.4484-27.8558-17.0366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-4 - 170
2X-RAY DIFFRACTION2chain BB5 - 164

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