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Yorodumi- PDB-5x7g: Crystal Structure of Paenibacillus sp. 598K cycloisomaltooligosac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x7g | ||||||
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Title | Crystal Structure of Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase | ||||||
Components | Cycloisomaltooligosaccharide glucanotransferase | ||||||
Keywords | TRANSFERASE / glydoside hydrolase family 66 / carbohydrate-binding module family 35 | ||||||
Function / homology | Function and homology information cycloisomaltooligosaccharide glucanotransferase / glycosyltransferase activity / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | Paenibacillus sp. 598K (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Fujimoto, Z. / Kishine, N. / Suzuki, N. / Suzuki, R. / Momma, M. / Funane, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biosci. Rep. / Year: 2017 Title: Isomaltooligosaccharide-binding structure ofPaenibacillussp. 598K cycloisomaltooligosaccharide glucanotransferase Authors: Fujimoto, Z. / Kishine, N. / Suzuki, N. / Suzuki, R. / Mizushima, D. / Momma, M. / Kimura, K. / Funane, K. #1: Journal: Biochim. Biophys. Acta / Year: 2012 Title: Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K Authors: Suzuki, R. / Terasawa, K. / Kimura, K. / Fujimoto, Z. / Momma, M. / Kobayashi, M. / Kimura, A. / Funane, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x7g.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x7g.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 5x7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x7g_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 5x7g_full_validation.pdf.gz | 466.2 KB | Display | |
Data in XML | 5x7g_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 5x7g_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/5x7g ftp://data.pdbj.org/pub/pdb/validation_reports/x7/5x7g | HTTPS FTP |
-Related structure data
Related structure data | 5x7hC 3wnkS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 80618.508 Da / Num. of mol.: 1 / Fragment: UNP residues 41-739 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. 598K (bacteria) / Strain: 598K / Gene: cit / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: G9MBW2, cycloisomaltooligosaccharide glucanotransferase |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: 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: 2.81 Å3/Da / Density % sol: 56.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% PEG3350, 12% Tacsimate |
-Data collection
Diffraction | Mean temperature: 95 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: Mar 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 46942 / % possible obs: 100 % / Redundancy: 22.1 % / Biso Wilson estimate: 33.366 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.021 / Χ2: 1.153 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 4611 / Rpim(I) all: 0.184 / Χ2: 1.316 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WNK Resolution: 2.2→98.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.808 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.182 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.419 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→98.45 Å
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Refine LS restraints |
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