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Open data
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Basic information
Entry | Database: PDB / ID: 7qqi | ||||||
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Title | Sucrose phosphorylase from Faecalibaculum rodentium | ||||||
![]() | Aamy domain-containing protein | ||||||
![]() | TRANSFERASE / sucrose phosphorylase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ubiparip, Z. / Capra, N. / Rozeboom, H.J. / Desmet, T. / Thunnissen, A.M.W.H. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Sucrose phosphorylase from Faecalibaculum rodentium Authors: Ubiparip, Z. / Capra, N. / Rozeboom, H.J. / Thunnissen, A.M.W.H. / Desmet, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 365 KB | Display | ![]() |
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PDB format | ![]() | 287.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.2 KB | Display | ![]() |
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Full document | ![]() | 421.1 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s9vS S: Starting model for refinement |
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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: 56898.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-TRS / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 ...Details: Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 M Na citrate, 0.1 M Tris, pH 7.0, 0.2 M NaCl |
-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: Nov 25, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.36→46 Å / Num. obs: 95834 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.056 / Rrim(I) all: 0.095 / Net I/σ(I): 10.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6S9V Resolution: 1.36→46 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.355 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.057 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.554 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→46 Å
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Refine LS restraints |
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LS refinement shell |
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