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- PDB-6gyw: Crystal structure of DacA from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6gyw
TitleCrystal structure of DacA from Staphylococcus aureus
ComponentsDiadenylate cyclase
KeywordsTRANSFERASE / c-di-AMP / diadenylate cyclase
Function / homologyYojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diadenylate cyclase
B: Diadenylate cyclase


Theoretical massNumber of molelcules
Total (without water)38,7982
Polymers38,7982
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-8 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.799, 68.190, 76.796
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


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M LiCl, 0.1M Na-Cacodylate pH 6.5, 30% Peg400

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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: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→68.19 Å / Num. obs: 32376 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 10 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2 / Num. unique obs: 1659 / CC1/2: 0.968 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RV7

4rv7


Resolution: 1.7→50.99 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.5
RfactorNum. reflection% reflection
Rfree0.2004 1616 5.01 %
Rwork0.1735 --
obs0.1749 32265 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.4 Å2 / Biso mean: 42.8617 Å2 / Biso min: 19.11 Å2
Refinement stepCycle: final / Resolution: 1.7→50.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 0 148 2472
Biso mean---45.69 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062362
X-RAY DIFFRACTIONf_angle_d0.9623191
X-RAY DIFFRACTIONf_chiral_restr0.038375
X-RAY DIFFRACTIONf_plane_restr0.004408
X-RAY DIFFRACTIONf_dihedral_angle_d13.595873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.75010.25281210.23142502262398
1.7501-1.80660.25011340.21324862620100
1.8066-1.87120.22611260.186825172643100
1.8712-1.94610.22931270.180725392666100
1.9461-2.03470.21171190.174225422661100
2.0347-2.14190.21571420.173625342676100
2.1419-2.27610.18881370.16525432680100
2.2761-2.45190.19451480.169425072655100
2.4519-2.69860.2371340.176725742708100
2.6986-3.0890.24651360.18925692705100
3.089-3.89170.18361470.175626042751100
3.8917-51.01280.1761450.160427322877100
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)
13.8660.405-0.1623.11950.07054.67290.1263-0.05840.3826-0.01260.02560.2026-0.5712-0.1456-0.13570.22410.03260.02150.182-0.01220.166420.543510.474514.9016
23.31211.44442.37563.13690.06582.90680.15320.0267-0.5042-0.23240.06620.00230.3805-0.1664-0.20380.2396-0.01-0.00680.2596-0.02870.248418.5896-2.507619.662
34.57911.5713-0.11593.49810.32765.5795-0.03270.2472-0.0402-0.27890.01790.1317-0.0867-0.56060.02870.22150.0279-0.05160.3258-0.01560.265912.23312.947810.2552
48.2439-0.0208-2.14235.4681-0.07789.7931-0.0848-0.4962-0.90030.2680.07390.1250.935-0.05340.05090.3095-0.0284-0.09930.21090.00430.438236.2977-7.669534.6619
57.1438-0.8375-0.7546.70921.11861.1062-0.11350.6928-0.5199-0.5152-0.0129-0.431-0.19490.493-0.00460.21880.016-0.01210.3051-0.06490.263243.02030.344927.6754
65.61080.50992.20292.82390.28253.5247-0.23090.12550.3352-0.04210.02050.0042-0.2142-0.14090.15830.23030.0327-0.05610.2028-0.03380.246734.13896.782930.5392
76.74381.23441.91852.33930.40042.8948-0.16340.90570.4635-0.19880.0667-0.8247-0.17160.89070.26580.3862-0.0655-0.05450.41350.01880.556151.578812.267530.2128
88.61961.16852.16095.25282.01398.8509-0.5565-0.1250.54130.11020.07190.0867-0.00180.29030.16580.3027-0.0888-0.12790.19540.02320.271949.127210.649132.7583
95.2703-0.54570.3384.41622.31056.1776-0.24070.35960.1328-0.1474-0.0394-0.1828-0.29420.39020.25410.2123-0.0162-0.06320.24730.0210.221547.60632.998533.6078
108.0345-1.14260.51872.16441.78165.6786-0.1098-0.12040.42640.3588-0.1123-0.3627-0.18220.4766-0.00120.29160.0066-0.0880.307-0.00310.28552.73981.618738.2333
112.3644-3.7374-0.05496.2094-0.39644.9265-0.1628-0.8929-0.78640.30980.2120.27040.43480.03940.05060.3171-0.0303-0.05130.36670.04660.319441.762-4.253242.2604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 110 through 139 )A110 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 206 )A140 - 206
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 260 )A207 - 260
4X-RAY DIFFRACTION4chain 'B' and (resid 111 through 130 )B111 - 130
5X-RAY DIFFRACTION5chain 'B' and (resid 131 through 139 )B131 - 139
6X-RAY DIFFRACTION6chain 'B' and (resid 140 through 188 )B140 - 188
7X-RAY DIFFRACTION7chain 'B' and (resid 189 through 206 )B189 - 206
8X-RAY DIFFRACTION8chain 'B' and (resid 207 through 217 )B207 - 217
9X-RAY DIFFRACTION9chain 'B' and (resid 218 through 237 )B218 - 237
10X-RAY DIFFRACTION10chain 'B' and (resid 238 through 246 )B238 - 246
11X-RAY DIFFRACTION11chain 'B' and (resid 247 through 261 )B247 - 261

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