+Open data
-Basic information
Entry | Database: PDB / ID: 7oml | ||||||
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Title | Bacillus subtilis phosphoglucomutase GlmM (metal bound) | ||||||
Components | Phosphoglucosamine mutase | ||||||
Keywords | ISOMERASE / Phosphoglucosamine Mutase / glucosamine-6-phosphate / glucosamine-1-phosphate / c-di-AMP / diadenylate cyclase / metal-bound protein. | ||||||
Function / homology | Function and homology information phosphoglucosamine mutase / phosphoglucosamine mutase activity / phosphomannomutase activity / UDP-N-acetylglucosamine biosynthetic process / peptidoglycan biosynthetic process / carbohydrate metabolic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 7oml.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oml.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 7oml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oml_validation.pdf.gz | 427.8 KB | Display | wwPDB validaton report |
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Full document | 7oml_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 7oml_validation.xml.gz | 17 KB | Display | |
Data in CIF | 7oml_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/7oml ftp://data.pdbj.org/pub/pdb/validation_reports/om/7oml | HTTPS FTP |
-Related structure data
Related structure data | 7ojrC 7ojsC 7olhC 3pdkS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 50314.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: glmM, ybbT, BSU01770 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34824, phosphoglucosamine mutase |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550 buffer |
-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: Oct 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.15 Å / Num. obs: 15955 / % possible obs: 98.8 % / Redundancy: 20.2 % / CC1/2: 0.99 / Rpim(I) all: 0.092 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.9→3.08 Å / Num. unique obs: 2503 / CC1/2: 0.39 / Rpim(I) all: 1.46 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Bacillus anthracis GlmM 3PDK Resolution: 2.9→48.149 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.76 / 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: 145.77 Å2 / Biso mean: 45.0009 Å2 / Biso min: 13.98 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→48.149 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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