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Yorodumi- PDB-6az5: Crystal structure of CBMd (family CBM41) from Eubacterium rectale... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6az5 | ||||||||||||
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Title | Crystal structure of CBMd (family CBM41) from Eubacterium rectale Amy13K | ||||||||||||
Components | alpha-amylase | ||||||||||||
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: 2.2 Å | ||||||||||||
Authors | Cockburn, D.W. / Wawrzak, Z. / Suh, C. / Koropatkin, N.M. | ||||||||||||
Funding support | United States, 3items
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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 | 6az5.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6az5.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 6az5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/6az5 ftp://data.pdbj.org/pub/pdb/validation_reports/az/6az5 | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 13025.083 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium rectale DSM 17629 (bacteria) Gene: EUR_21100 / Production host: Escherichia coli (E. coli) / References: UniProt: D6DYI9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50% pentaerythritol propoxylate (5/4 PO/OH), 0.1 M Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33.28 Å / Num. obs: 6492 / % possible obs: 99.94 % / Redundancy: 16.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07451 / Rpim(I) all: 0.01875 / Net I/σ(I): 15.08 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 17.6 % / Rmerge(I) obs: 0.1759 / Mean I/σ(I) obs: 9.98 / Num. unique obs: 608 / CC1/2: 0.996 / Rpim(I) all: 0.04297 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→33.28 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→33.28 Å
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Refine LS restraints |
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LS refinement shell |
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