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Open data
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Basic information
Entry | Database: PDB / ID: 1o8p | ||||||
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Title | Unbound structure of CsCBM6-3 from Clostridium stercorarium | ||||||
![]() | PUTATUVE ENDO-XYLANASE | ||||||
![]() | HYDROLASE / CARBOHYDRATE-BINDING MODULE / XYLAN / CELLULOSE / BETA- SANDWICH / GLYCOSIDASE / XYLAN DEGRADATION | ||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Boraston, A.B. / Notenboom, V. / Warren, R.A.J. / Kilbrun, D.G. / Rose, D.R. / Davies, G.J. | ||||||
![]() | ![]() Title: Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains. Authors: Boraston, A.B. / Notenboom, V. / Warren, R.A. / Kilburn, D.G. / Rose, D.R. / Davies, G. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.6 KB | Display | ![]() |
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PDB format | ![]() | 27.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.2 KB | Display | ![]() |
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Full document | ![]() | 423.6 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1naeC ![]() 1o8sC ![]() 1od3C ![]() 1gmmS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 15516.851 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING DOMAIN, RESIDUES 273-417 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q93AQ5, UniProt: Q8GJ44*PLUS, endo-1,4-beta-xylanase |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Sequence details | C-TERMINAL MODULE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.60 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→40 Å / Num. obs: 8498 / % possible obs: 79.2 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 5 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 6.6 / % possible all: 27.5 |
Reflection | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 40 Å / % possible obs: 95.9 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 2.12 Å / % possible obs: 95.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GMM Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.854 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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