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Yorodumi- PDB-6d5c: Structure of Caldicellulosiruptor danielii GH10 module of glycosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d5c | ||||||
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Title | Structure of Caldicellulosiruptor danielii GH10 module of glycoside hydrolase WP_045175321 | ||||||
Components | glycoside hydrolase WP_045175321 | ||||||
Keywords | HYDROLASE / GH10 / glycoside hydrolase | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Caldicellulosiruptor sp. Wai35.B1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 6d5c.cif.gz | 257.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d5c.ent.gz | 207.4 KB | Display | PDB format |
PDBx/mmJSON format | 6d5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/6d5c ftp://data.pdbj.org/pub/pdb/validation_reports/d5/6d5c | HTTPS FTP |
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-Related structure data
Related structure data | 6d5bC 6d5dC 5ay7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 40651.699 Da / Num. of mol.: 3 / Fragment: GH10 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: A0A4V8GZQ8*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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-Non-polymers , 5 types, 1313 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-FMT / | #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: 2.75 Å3/Da / Density % sol: 55.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8-9, 1.5-2.1 M ammonium sulfate |
-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: May 31, 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: 104001 / % possible obs: 100 % / Redundancy: 6.03 % / Rsym value: 0.068 / Net I/σ(I): 14.32 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.54 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 14807 / Rsym value: 0.4469 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5AY7 Resolution: 1.9→86.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.029 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.144 / 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: 27.186 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→86.48 Å
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Refine LS restraints |
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