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Yorodumi- PDB-6klf: Crystal structure of branching enzyme D434A mutant from Cyanothec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6klf | |||||||||
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Title | Crystal structure of branching enzyme D434A mutant from Cyanothece sp. ATCC 51142 | |||||||||
Components | 1,4-alpha-glucan branching enzyme GlgB | |||||||||
Keywords | TRANSFERASE / starch-producing cyanobacteria / inactive mutant | |||||||||
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 | Crocosphaera subtropica ATCC 51142 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Suzuki, R. / Suzuki, E. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2021 Title: Cyanobacterial branching enzymes bind to alpha-glucan via surface binding sites Authors: El Mannai, Y. / Deto, R. / Kuroki, M. / Suzuki, R. / Suzuki, E. #1: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6klf.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6klf.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 6klf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6klf_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 6klf_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 6klf_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 6klf_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/6klf ftp://data.pdbj.org/pub/pdb/validation_reports/kl/6klf | HTTPS FTP |
-Related structure data
Related structure data | 5gqxS 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: 88518.930 Da / Num. of mol.: 1 / Mutation: D434A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Crocosphaera subtropica ATCC 51142 (bacteria) Strain: ATCC 51142 / Gene: glgB, glgB1, cce_2248 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: B1WPM8, 1,4-alpha-glucan branching enzyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.67 Å3/Da / Density % sol: 73.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 8%(w/v) ethanol, 0.1 M HEPES-NaOH pH 7.2, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: May 25, 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: 2.5→50 Å / Num. obs: 58556 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.365 / Num. unique obs: 2880 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GQX Resolution: 2.5→47.29 Å / Cross valid method: FREE R-VALUE
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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 |
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Refinement step | Cycle: LAST / Resolution: 2.5→47.29 Å
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LS refinement shell | Resolution: 2.5→2.565 Å
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