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Yorodumi- PDB-1w9t: Structure of a beta-1,3-glucan binding CBM6 from Bacillus halodur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w9t | |||||||||
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Title | Structure of a beta-1,3-glucan binding CBM6 from Bacillus halodurans in complex with xylobiose | |||||||||
Components | BH0236 PROTEIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / CARBOHYDRATE-BINDING MODULE / LECTIN / BETA-GLUCAN / CARBOHYDRATE BINDING / GLYCOSIDE HYDROLASE | |||||||||
Function / homology | Function and homology information : / endo-1,3(4)-beta-glucanase activity / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / polysaccharide catabolic process / cell wall organization / carbohydrate binding / cell surface / extracellular region Similarity search - Function | |||||||||
Biological species | BACILLUS HALODURANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | |||||||||
Authors | Boraston, A.B. / van Bueren, A.L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Family 6 Carbohydrate Binding Modules Recognize the Non-Reducing End of Beta-1,3-Linked Glucans by Presenting a Unique Ligand Binding Surface Authors: Van Bueren, A.L. / Moreland, C. / Gilbert, H.J. / Boraston, A.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w9t.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w9t.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 1w9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w9t_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1w9t_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1w9t_validation.xml.gz | 18 KB | Display | |
Data in CIF | 1w9t_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/1w9t ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w9t | HTTPS FTP |
-Related structure data
Related structure data | 1w9sC 1w9wC 1gmmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15673.985 Da / Num. of mol.: 2 / Fragment: CBM, RESIDUES 790-925 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KG76 |
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-Sugars , 3 types, 8 molecules
#2: Polysaccharide | #4: Sugar | #5: Sugar | ChemComp-XYP / |
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-Non-polymers , 2 types, 378 molecules
#3: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.62 % |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / 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: 1.62→20 Å / Num. obs: 27417 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.5 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GMM Resolution: 1.62→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.804 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→20 Å
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Refine LS restraints |
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