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Yorodumi- PDB-5wu7: Crystal structure of GH57-type branching enzyme from hyperthermop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wu7 | ||||||
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Title | Crystal structure of GH57-type branching enzyme from hyperthermophilic archaeon Pyrococcus horikoshii | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / enzyme / amylase / glycogen branching enzyme | ||||||
Function / homology | Function and homology information alpha-glucan biosynthetic process / 1,4-alpha-glucan branching enzyme activity Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Na, S. / Jo, I. / Ha, N.-C. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structural basis for the transglycosylase activity of a GH57-type glycogen branching enzyme from Pyrococcus horikoshii. Authors: Na, S. / Park, M. / Jo, I. / Cha, J. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wu7.cif.gz | 228.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wu7.ent.gz | 183.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/5wu7 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/5wu7 | HTTPS FTP |
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-Related structure data
Related structure data | 3n8tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 66938.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GOL Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH1386 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O50094 #2: Chemical | #3: 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: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.3 Details: 20 mM citric acid, 10% (w/v) PEG 3350, 80 mM Bis-Tris propane pH 9.3, 2 mM tris (2-carboxyethyl) phosphine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.521 Å / Num. obs: 44048 / % possible obs: 95 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.08 / % possible all: 72.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N8T Resolution: 2.31→33.521 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 26.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→33.521 Å
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Refine LS restraints |
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LS refinement shell |
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