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- PDB-7ojs: Complex structure 2 of the Bacillus subtilis CdaA c-di-AMP cyclas... -

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Basic information

Entry
Database: PDB / ID: 7ojs
TitleComplex structure 2 of the Bacillus subtilis CdaA c-di-AMP cyclase domain (CdaACD) and the phosphoglucomutase GlmM short variant (GlmMF369)
Components
  • Cyclic di-AMP synthase CdaA
  • Phosphoglucosamine mutase
KeywordsPROTEIN BINDING / Phosphoglucosamine Mutase / glucosamine-6-phosphate / glucosamine-1-phosphate / c-di-AMP / diadenylate cyclase / protein complex / GlmM / CdaA / DacA / protein protein complex / isomerase / heterodimer
Function / homology
Function and homology information


phosphoglucosamine mutase / phosphoglucosamine mutase activity / phosphomannomutase activity / diadenylate cyclase / diadenylate cyclase activity / UDP-N-acetylglucosamine biosynthetic process / cAMP biosynthetic process / adenylate cyclase activity / peptidoglycan biosynthetic process / carbohydrate metabolic process ...phosphoglucosamine mutase / phosphoglucosamine mutase activity / phosphomannomutase activity / diadenylate cyclase / diadenylate cyclase activity / UDP-N-acetylglucosamine biosynthetic process / cAMP biosynthetic process / adenylate cyclase activity / peptidoglycan biosynthetic process / carbohydrate metabolic process / magnesium ion binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
Phosphoglucosamine mutase, bacterial type / : / Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / Alpha-D-phosphohexomutase, C-terminal / : / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily ...Phosphoglucosamine mutase, bacterial type / : / Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / Alpha-D-phosphohexomutase, C-terminal / : / 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. / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
Similarity search - Domain/homology
Phosphoglucosamine mutase / Cyclic di-AMP synthase CdaA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsPathania, M. / Grundling, A.G. / Freemont, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)P63775 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM.
Authors: Pathania, M. / Tosi, T. / Millership, C. / Hoshiga, F. / Morgan, R.M.L. / Freemont, P.S. / Grundling, A.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Phosphoglucosamine mutase
F: Phosphoglucosamine mutase
H: Cyclic di-AMP synthase CdaA
I: Cyclic di-AMP synthase CdaA
A: Phosphoglucosamine mutase
B: Phosphoglucosamine mutase
D: Cyclic di-AMP synthase CdaA
E: Cyclic di-AMP synthase CdaA
G: Phosphoglucosamine mutase
J: Phosphoglucosamine mutase
K: Cyclic di-AMP synthase CdaA
L: Cyclic di-AMP synthase CdaA


Theoretical massNumber of molelcules
Total (without water)347,69712
Polymers347,69712
Non-polymers00
Water00
1
C: Phosphoglucosamine mutase
F: Phosphoglucosamine mutase
H: Cyclic di-AMP synthase CdaA
I: Cyclic di-AMP synthase CdaA


Theoretical massNumber of molelcules
Total (without water)115,8994
Polymers115,8994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphoglucosamine mutase
B: Phosphoglucosamine mutase
D: Cyclic di-AMP synthase CdaA
E: Cyclic di-AMP synthase CdaA


Theoretical massNumber of molelcules
Total (without water)115,8994
Polymers115,8994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Phosphoglucosamine mutase
J: Phosphoglucosamine mutase
K: Cyclic di-AMP synthase CdaA
L: Cyclic di-AMP synthase CdaA


Theoretical massNumber of molelcules
Total (without water)115,8994
Polymers115,8994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.805, 228.536, 153.194
Angle α, β, γ (deg.)90.000, 99.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphoglucosamine mutase


Mass: 39506.547 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: glmM, ybbT, BSU01770 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34824, phosphoglucosamine mutase
#2: Protein
Cyclic di-AMP synthase CdaA / c-di-AMP synthase / Diadenylate cyclase / DAC


Mass: 18442.963 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: cdaA, ybbP, BSU01750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45589, diadenylate cyclase

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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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M carboxylic acids, 0.1 M buffer system 1 (Imidazole; MES, pH 6.5) and 30% GOL_P4K (60% glycerol, PEG 4K)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 4.2→76.18 Å / Num. obs: 31005 / % possible obs: 99.9 % / Redundancy: 3.8 % / CC1/2: 0.78 / Rpim(I) all: 0.062 / Net I/σ(I): 2.1
Reflection shellResolution: 4.2→75.46 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 30768 / CC1/2: 0.39 / Rpim(I) all: 0.223

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dimers of Bacillus subtilis CdaACD and GlmMF369 structures

Resolution: 4.2→75.466 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2955 1497 4.87 %
Rwork0.226 29271 -
obs0.2294 30768 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.79 Å2 / Biso min: 51.91 Å2
Refinement stepCycle: final / Resolution: 4.2→75.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23190 0 0 0 23190
Num. residues----3084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.2-4.33560.30471020.287259398
4.3356-4.49050.40241320.2796270098
4.4905-4.67030.33651250.2693260499
4.6703-4.88280.35891410.2728266299
4.8828-5.14020.32061450.26272651100
5.1402-5.46210.34181460.2599263399
5.4621-5.88370.28981310.26052680100
5.8837-6.47550.32761530.24392664100
6.4755-7.41180.30531470.23112673100
7.4118-9.33540.23921260.15962704100
9.3354-75.460.21491490.1505270799

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