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- PDB-5gqu: Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gqu | ||||||||||||
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Title | Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142 | ||||||||||||
![]() | 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 / 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: Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model 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 | ![]() | 194.7 KB | Display | ![]() |
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PDB format | ![]() | 150.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 463.4 KB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 59.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gqvC ![]() 5gqwC ![]() 5gqxC ![]() 1m7xS C: citing same article ( S: Starting model for refinement |
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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
#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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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.68 Å3/Da / Density % sol: 73.74 % |
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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: 1.85→50 Å / Num. obs: 143511 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 61 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 10.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1M7X Resolution: 1.85→47.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.441 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.695 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→47.29 Å
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