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Yorodumi- PDB-6b15: Crystal structure of CBMbc (family CBM26) from Eubacterium rectal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b15 | ||||||
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Title | Crystal structure of CBMbc (family CBM26) from Eubacterium rectale Amy13K | ||||||
Components | Amy13K | ||||||
Keywords | SUGAR BINDING PROTEIN / Carbohydrate Binding Module / Amylase / Starch / Gut Microbiome / Eubacterium rectale | ||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process / membrane Similarity search - Function | ||||||
Biological species | Eubacterium rectale DSM 17629 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Cockburn, D.W. / Wawrzak, Z. / Perez Medina, K. / Koropatkin, N.M. | ||||||
Citation | Journal: Mol. Microbiol. / Year: 2018 Title: Novel carbohydrate binding modules in the surface anchored alpha-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut. Authors: Cockburn, D.W. / Suh, C. / Medina, K.P. / Duvall, R.M. / Wawrzak, Z. / Henrissat, B. / Koropatkin, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b15.cif.gz | 311.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b15.ent.gz | 255 KB | Display | PDB format |
PDBx/mmJSON format | 6b15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/6b15 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b15 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22953.947 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium rectale DSM 17629 (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: D6DYI9 #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: 4.14 Å3/Da / Density % sol: 70.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% Tacsimate, 0.1 M Bis-Tris Propane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→36.02 Å / Num. obs: 86483 / % possible obs: 98.46 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09175 / Rpim(I) all: 0.03852 / Net I/σ(I): 7.86 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5615 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 8664 / CC1/2: 0.832 / Rpim(I) all: 0.237 / % possible all: 99.38 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→36.02 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→36.02 Å
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Refine LS restraints |
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LS refinement shell |
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