Computational protocol: Isomaltooligosaccharide-binding structure of Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase

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Protocol publication

[…] Diffraction experiments for protein crystals were conducted at the beamline BL-NW12 of the Photon Factory Advanced Ring (PF-AR), High Energy Accelerator Research Organization, Tsukuba, Japan []. The crystal was scooped in a nylon cryoloop (0.3 mm, Hampton Research) and then flash-cooled under a nitrogen stream at 95 K. Diffraction data by synchrotron radiation were collected at a wavelength of 1.0000 Å with a Quantum 270 CCD detector (Area Detector Systems Corp., Poway, CA, U.S.A.). The data were integrated and scaled using the programs DENZO and SCALEPACK in the HKL2000 program suite []. For the CI-7 complex data, 0.5 μl precipitant solution containing 5% CI-7 was added into the crystal drop for 3 min before data collection.The crystal structure was determined by the molecular replacement method using the structure of PaCITase (PDB code: 3WNK, []) as the template structure using the program MolRep [] incorporated in the CCP4 program suite []. Manual model building and molecular refinement were performed using COOT [] and REFMAC5 []. Data collection and refinement statistics are shown in . Model stereochemistry was determined with the program RAMGAGE []. Structural illustrations were drawn with the program CueMol2 (http://cuemol.sourceforge.jp/en/). […]

Pipeline specifications

Software tools Molrep, CCP4, Coot, REFMAC5, CueMol
Application Protein structure analysis
Chemicals Carbohydrates, Glucose