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Yorodumi- PDB-5gr6: Crystal structure of branching enzyme Y500A/D501A double mutant f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gr6 | ||||||||||||
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Title | Crystal structure of branching enzyme Y500A/D501A double mutant from Cyanothece sp. ATCC 51142 | ||||||||||||
Components | 1,4-alpha-glucan branching enzyme GlgB | ||||||||||||
Keywords | TRANSFERASE / branching enzyme / glycoside hydrolase family 13 / cyanobacteria / starch | ||||||||||||
Function / homology | Function and homology information starch metabolic process / 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 / cytosol Similarity search - Function | ||||||||||||
Biological species | Cyanothece sp. | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Suzuki, R. / Suzuki, E. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: To be published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gr6.cif.gz | 192.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gr6.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gr6_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 5gr6_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 5gr6_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 5gr6_validation.cif.gz | 55.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/5gr6 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/5gr6 | HTTPS FTP |
-Related structure data
Related structure data | 5gqyC 5gqzSC 5gr0C 5gr1C 5gr2C 5gr3C 5gr4C 5gr5C C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 92550.320 Da / Num. of mol.: 1 / Mutation: Y500A, D501A 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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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 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: 112602 / % possible obs: 100 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 60.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 10.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GQZ Resolution: 2→46.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.301 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.102 / 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: 28.171 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.06 Å
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