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- PDB-7u3b: Structure of S. venezuelae GlgX bound to c-di-GMP and acarbose (p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u3b | ||||||
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Title | Structure of S. venezuelae GlgX bound to c-di-GMP and acarbose (pH 8.5) | ||||||
![]() | Glycogen debranching enzyme GlgX | ||||||
![]() | HYDROLASE / GlgX / glycogen / acarbose / c-di-GMP / Streptomyces | ||||||
Function / homology | ![]() glycogen debranching enzyme activity / glycogen catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Schumacher, M.A. / Tschowri, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP. Authors: Schumacher, M.A. / Wormann, M.E. / Henderson, M. / Salinas, R. / Latoscha, A. / Al-Bassam, M.M. / Singh, K.S. / Barclay, E. / Gunka, K. / Tschowri, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 895.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7u39C ![]() 7u3aSC ![]() 7u3dC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 80167.234 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-A16 / #3: Chemical | ChemComp-C2E / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 50% MPD, 0.1 M Tris pH 8.5 and 200 mM ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→48.5 Å / Num. obs: 83324 / % possible obs: 98.2 % / Redundancy: 1.7 % / CC1/2: 0.923 / Rpim(I) all: 0.17 / Rsym value: 0.199 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 3.6→3.78 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5752 / CC1/2: 0.667 / Rpim(I) all: 0.517 / Rsym value: 0.78 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 7U3A Resolution: 3.6→48.5 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.67 / 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: 216.7 Å2 / Biso mean: 46.8686 Å2 / Biso min: 0.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.6→48.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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