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- PDB-7qf7: Orthorhombic crystal structure of PTG CBM21 in complex with beta-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qf7 | ||||||
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Title | Orthorhombic crystal structure of PTG CBM21 in complex with beta-cyclodextrin | ||||||
![]() | Protein phosphatase 1 regulatory subunit 3C | ||||||
![]() | SUGAR BINDING PROTEIN / carbohydrate binding / immunoglobulin-like fold | ||||||
Function / homology | ![]() glycogen binding / protein phosphatase type 1 complex / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / glycogen biosynthetic process / protein serine/threonine phosphatase activity / glycogen metabolic process / Myoclonic epilepsy of Lafora / Glycogen synthesis / protein phosphatase binding ...glycogen binding / protein phosphatase type 1 complex / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / glycogen biosynthetic process / protein serine/threonine phosphatase activity / glycogen metabolic process / Myoclonic epilepsy of Lafora / Glycogen synthesis / protein phosphatase binding / molecular adaptor activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Semrau, M.S. / Storici, P. / Lolli, G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Molecular architecture of the glycogen- committed PP1/PTG holoenzyme. Authors: Semrau, M.S. / Giachin, G. / Covaceuszach, S. / Cassetta, A. / Demitri, N. / Storici, P. / Lolli, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7qfaC ![]() 7qfbC ![]() 7qm2C ![]() 2eefS 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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Unit cell |
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Components
#1: Protein | Mass: 15647.529 Da / Num. of mol.: 1 / Fragment: CBM21 domain (residues 132-264) / Mutation: First residue S derives from the expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % / Mosaicity: 0.16 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 3 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9718 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.47→44.074 Å / Num. obs: 26941 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 17.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2EEF Resolution: 1.47→44.074 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.96 / 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: 86.34 Å2 / Biso mean: 33.8912 Å2 / Biso min: 17.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.47→44.074 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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