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- PDB-6d5d: Structure of Caldicellulosiruptor danielii GH48 module of glycosi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d5d | |||||||||
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Title | Structure of Caldicellulosiruptor danielii GH48 module of glycoside hydrolase WP_045175321 | |||||||||
![]() | glycoside hydrolase WP_045175321 | |||||||||
![]() | HYDROLASE / GH48 / glycoside hydrolase | |||||||||
Function / homology | ![]() Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulase activity / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Alahuhta, P.M. / Lunin, V.V. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.7 KB | Display | ![]() |
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PDB format | ![]() | 125.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 51.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d5bC ![]() 6d5cC ![]() 4el8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 73792.945 Da / Num. of mol.: 1 / Fragment: GH48 module Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A4V8GZQ9*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||||
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#2: Polysaccharide | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M citric acid, pH 5-6, 20% 2-propanol, 0.05 M trisodium citrate, 14-25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 53369 / % possible obs: 99.2 % / Redundancy: 5.35 % / Rpim(I) all: 0.0613 / Net I/σ(I): 9.95 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.99 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 7332 / Rpim(I) all: 0.3521 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4EL8 Resolution: 1.9→103.08 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.149 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.155 / 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: 24.103 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→103.08 Å
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Refine LS restraints |
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