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Yorodumi- PDB-5gqv: Crystal structure of branching enzyme from Cyanothece sp. ATCC 51... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gqv | ||||||||||||
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Title | Crystal structure of branching enzyme from Cyanothece sp. ATCC 51142 in complex with maltohexaose | ||||||||||||
Components | 1,4-alpha-glucan branching enzyme GlgB | ||||||||||||
Keywords | TRANSFERASE / branching enzyme / glycoside hydrolase family 13 / cyanobacteria / starch | ||||||||||||
Function / homology | Function and homology information 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Cyanothece sp. | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||||||||
Authors | Suzuki, R. / Suzuki, E. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J. Biol. Chem. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gqv.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gqv.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gqv_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5gqv_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5gqv_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 5gqv_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/5gqv ftp://data.pdbj.org/pub/pdb/validation_reports/gq/5gqv | HTTPS FTP |
-Related structure data
Related structure data | 5gquSC 5gqwC 5gqxC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Cyanothece sp. (strain ATCC 51142) (bacteria) Strain: ATCC 51142 / Gene: glgB, glgB1, cce_2248 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: B1WPM8, 1,4-alpha-glucan branching enzyme |
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-Sugars , 4 types, 8 molecules
#2: Polysaccharide | #3: Polysaccharide | #4: Polysaccharide | #5: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 169 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.58 Å3/Da / Density % sol: 73.2 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 15, 2015 |
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: 3→50 Å / Num. obs: 34353 / % possible obs: 99.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 40.17 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 15.12 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GQU Resolution: 3→47.42 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.899 / SU B: 10.618 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.578 / ESU R Free: 0.314 / 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: 39.693 Å2
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Refinement step | Cycle: LAST / Resolution: 3→47.42 Å
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