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Yorodumi- PDB-7ojs: Complex structure 2 of the Bacillus subtilis CdaA c-di-AMP cyclas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ojs | ||||||
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Title | Complex structure 2 of the Bacillus subtilis CdaA c-di-AMP cyclase domain (CdaACD) and the phosphoglucomutase GlmM short variant (GlmMF369) | ||||||
Components |
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Keywords | PROTEIN 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 activity / diadenylate cyclase / : / UDP-N-acetylglucosamine biosynthetic process / cAMP biosynthetic process / adenylate cyclase activity / peptidoglycan biosynthetic process ...phosphoglucosamine mutase / phosphoglucosamine mutase activity / phosphomannomutase activity / diadenylate cyclase activity / diadenylate cyclase / : / 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 | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | Pathania, M. / Grundling, A.G. / Freemont, P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ojs.cif.gz | 569.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ojs.ent.gz | 477.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ojs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/7ojs ftp://data.pdbj.org/pub/pdb/validation_reports/oj/7ojs | HTTPS FTP |
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-Related structure data
Related structure data | 7ojrC 7olhC 7omlC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | 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 | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.39 % |
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Crystal grow | Temperature: 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) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: DIAMOND / Beamline: I03 / Wavelength: 0.99 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 199.79 Å2 / Biso min: 51.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.2→75.466 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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