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Yorodumi- PDB-1uy2: Binding sub-site dissection of a family 6 carbohydrate-binding mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uy2 | |||||||||
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Title | Binding sub-site dissection of a family 6 carbohydrate-binding module by X-ray crystallography and isothermal titration calorimetry | |||||||||
Components | ENDO-1,4-BETA-XYLANASE A | |||||||||
Keywords | CARBOHYDRATE-BINDING MODULE / THERMODYNAMICS / PROTEIN STRUCTURE / XYLAN / PROTEIN-CARBOHYDRATE INTERACTIONS | |||||||||
Function / homology | Function and homology information 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 | CLOSTRIDIUM STERCORARIUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Van Bueren, A.L. / Boraston, A.B. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Binding Sub-Site Dissection of a Carbohydrate-Binding Module Reveals the Contribution of Entropy to Oligosaccharide Recognition at "Non-Primary" Binding Subsites. Authors: Van Bueren, A.L. / Boraston, A.B. | |||||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uy2.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uy2.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 1uy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uy2_validation.pdf.gz | 749.8 KB | Display | wwPDB validaton report |
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Full document | 1uy2_full_validation.pdf.gz | 750.8 KB | Display | |
Data in XML | 1uy2_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1uy2_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/1uy2 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/1uy2 | HTTPS FTP |
-Related structure data
Related structure data | 1uy1C 1uy3C 1uy4C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 15240.524 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 1-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM STERCORARIUM (bacteria) / Strain: NCIB 11745 / Plasmid: PET-CBM6-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93AQ5, UniProt: Q8GJ44*PLUS |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose |
-Non-polymers , 4 types, 162 molecules
#3: Chemical | ChemComp-NA / |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | pH: 4.5 / Details: pH 4.50 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS IV++ / Detector: IMAGE PLATE / Details: OSMIC BLUE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 18015 / % possible obs: 99.6 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GMM Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.81 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.086 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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