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- PDB-6gyx: Crystal structure of DacA from Staphylococcus aureus in complex w... -

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Basic information

Entry
Database: PDB / ID: 6gyx
TitleCrystal structure of DacA from Staphylococcus aureus in complex with ApCpp
ComponentsDiadenylate cyclase
KeywordsTRANSFERASE / c-di-AMP / diadenylate cyclase / ApCpp
Function / homologyYojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / 3-Layer(aba) Sandwich / Alpha Beta / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTosi, T. / Freemont, P.S. / Grundling, A.
CitationJournal: PLoS Pathog. / Year: 2019
Title: Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM.
Authors: Tosi, T. / Hoshiga, F. / Millership, C. / Singh, R. / Eldrid, C. / Patin, D. / Mengin-Lecreulx, D. / Thalassinos, K. / Freemont, P. / Grundling, A.
History
DepositionJul 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Diadenylate cyclase
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8635
Polymers38,7982
Non-polymers1,0653
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-10 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.092, 80.424, 96.195
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 111 through 215 or resid 217 through 260))
21(chain B and (resid 111 through 204 or resid 206 through 215 or resid 217 through 260))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILE(chain A and (resid 111 through 215 or resid 217 through 260))AB111 - 21517 - 121
12GLUGLUGLYGLY(chain A and (resid 111 through 215 or resid 217 through 260))AB217 - 260123 - 166
21SERSERSERSER(chain B and (resid 111 through 204 or resid 206 through 215 or resid 217 through 260))BA111 - 20417 - 110
22GLYGLYILEILE(chain B and (resid 111 through 204 or resid 206 through 215 or resid 217 through 260))BA206 - 215112 - 121
23GLUGLUGLYGLY(chain B and (resid 111 through 204 or resid 206 through 215 or resid 217 through 260))BA217 - 260123 - 166

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Components

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


Mass: 19399.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dacA, C7J94_12115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P7CAT2, diadenylate cyclase
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn

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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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mM MgCl2, 50 mM MES pH 5.8, 0.2M KCl, 3% Peg8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→61.7 Å / Num. obs: 10930 / % possible obs: 99.3 % / Redundancy: 12.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Net I/σ(I): 10.2
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.115 / Mean I/σ(I) obs: 2 / Num. unique obs: 1291 / CC1/2: 0.825 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GYW

6gyw


Resolution: 2.6→41.279 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.11
RfactorNum. reflection% reflection
Rfree0.2576 556 5.1 %
Rwork0.2313 --
obs0.2328 10899 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 226.78 Å2 / Biso mean: 101.1255 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.6→41.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 91 0 2416
Biso mean--144.06 --
Num. residues----301
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1591X-RAY DIFFRACTION12.708TORSIONAL
12B1591X-RAY DIFFRACTION12.708TORSIONAL

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