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- PDB-5gqy: Crystal structure of branching enzyme from Cyanothece sp. ATCC 51... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gqy | ||||||||||||
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Title | Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142 in complex with maltoheptaose | ||||||||||||
![]() | 1,4-alpha-glucan branching enzyme GlgB | ||||||||||||
![]() | TRANSFERASE / branching enzyme / glycoside hydrolase family 13 / cyanobacteria / starch | ||||||||||||
Function / homology | ![]() 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) / 1,4-alpha-glucan branching enzyme activity / starch metabolic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Cyanothece sp. | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Suzuki, R. / Suzuki, E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for substrate binding and catalysis of branching enzyme from Cyanothece sp. ATCC 51142 Authors: Hayashi, M. / Suzuki, R. / Colleoni, C. / Ball, S.G. / Fujita, N. / Suzuki, E. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: Crystallization and crystallographic analysis of branching enzymes from Cyanothece sp. ATCC 51142. Authors: Hayashi, M. / Suzuki, R. / Colleoni, C. / Ball, S.G. / Fujita, N. / Suzuki, E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.6 KB | Display | ![]() |
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PDB format | ![]() | 154.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 38.1 KB | Display | |
Data in CIF | ![]() | 57.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gqzC ![]() 5gr0C ![]() 5gr1C ![]() 5gr2C ![]() 5gr3C ![]() 5gr4C ![]() 5gr5C ![]() 5gr6C ![]() 5gquS S: Starting model for refinement 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 92686.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 51142 / Gene: glgB, glgB1, cce_2248 / Plasmid: pET15B / Production host: ![]() ![]() References: UniProt: B1WPM8, 1,4-alpha-glucan branching enzyme |
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-Sugars , 3 types, 7 molecules
#2: Polysaccharide | #3: Polysaccharide | #4: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 629 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: magnesium chloride, ethanol, HEPES-NaOH / PH range: 7.2 - 7.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 113447 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 63.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 9.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GQU Resolution: 2→47.38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.133 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.757 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.38 Å
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Refine LS restraints |
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