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Yorodumi- PDB-6d5b: Structure of Caldicellulosiruptor danielii CBM3 module of glycosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d5b | ||||||
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Title | Structure of Caldicellulosiruptor danielii CBM3 module of glycoside hydrolase WP_045175321 | ||||||
Components | glycoside hydrolase WP_045175321 | ||||||
Keywords | SUGAR BINDING PROTEIN / CBM3 / carbohydrate binding | ||||||
Function / homology | Function and homology information Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Caldicellulosiruptor sp. Wai35.B1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Alahuhta, P.M. / Lunin, V.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: AIChE J. / Year: 2019 Title: Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species Authors: Conway, J.M. / Crosby, J.R. / Hren, A.P. / Southerland, R.T. / Lee, L.L. / Lunin, V.V. / Alahuhta, P.M. / Himmel, M.E. / Bomble, Y.J. / Adams, M.W.W. / Kelly, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d5b.cif.gz | 419.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d5b.ent.gz | 338.6 KB | Display | PDB format |
PDBx/mmJSON format | 6d5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/6d5b ftp://data.pdbj.org/pub/pdb/validation_reports/d5/6d5b | HTTPS FTP |
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-Related structure data
Related structure data | 6d5cC 6d5dC 3zqwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 18958.756 Da / Num. of mol.: 12 / Fragment: CBM3 module Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor sp. Wai35.B1 (bacteria) Production host: Escherichia coli (E. coli) References: UniProt: A0A4V8GZQ7*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | ChemComp-CA / #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: 2.44 Å3/Da / Density % sol: 49.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 8% Tacsimate, pH 4-5, 14-25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jun 6, 2016 / Details: HELIOS MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 144145 / % possible obs: 99.1 % / Redundancy: 5.22 % / Rsym value: 0.1233 / Net I/σ(I): 7.64 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.72 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 19299 / Rpim(I) all: 0.7277 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3ZQW Resolution: 2→85.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.383 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.174 / 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: 27.522 Å2
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Refinement step | Cycle: 1 / Resolution: 2→85.91 Å
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Refine LS restraints |
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