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- PDB-7ojs: Complex structure 2 of the Bacillus subtilis CdaA c-di-AMP cyclas... -
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Open data
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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) | ||||||
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![]() | 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 | ![]() 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 ...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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pathania, M. / Grundling, A.G. / Freemont, P. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 573 KB | Display | ![]() |
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PDB format | ![]() | 469.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 520.7 KB | Display | ![]() |
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Full document | ![]() | 571 KB | Display | |
Data in XML | ![]() | 105.3 KB | Display | |
Data in CIF | ![]() | 140.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ojrC ![]() 7olhC ![]() 7omlC C: citing same article ( |
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Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: 168 / Gene: glmM, ybbT, BSU01770 / Production host: ![]() ![]() #2: Protein | Mass: 18442.963 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: cdaA, ybbP, BSU01750 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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