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Yorodumi- PDB-1uxx: CBM6ct from Clostridium thermocellum in complex with xylopentaose -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uxx | |||||||||
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Title | CBM6ct from Clostridium thermocellum in complex with xylopentaose | |||||||||
Components | XYLANASE U | |||||||||
Keywords | CARBOHYDRATE BINDING MODULE / CBM6 / XYLOPENTAOSE BINDING / XYLAN DEGRADATION | |||||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Czjzek, M. / Pires, V.M.R. / Henshaw, J. / Prates, J.A.M. / Henrissat, D.B.B. / Gilbert, H.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The Crystal Structure of the Family 6 Carbohydrate Binding Module from Cellvibrio Mixtus Endoglucanase 5A in Complex with Oligosaccharides Reveals Two Distinct Binding Sites with Different Ligand Specificities Authors: Pires, V.M.R. / Henshaw, J. / Prates, J.A.M. / Bolam, D. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Henrissat, B. / Planas, A. / Gilbert, H.J. / Czjzek, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uxx.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uxx.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1uxx ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1uxx | HTTPS FTP |
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-Related structure data
Related structure data | 1uxzC 1uy0C 1uyxC 1uyyC 1uyzC 1uz0C 1gmmS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14115.347 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 248-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O52780, endo-1,4-beta-xylanase |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Compound details | CATALYSES THE ENDOHYDROLYSIS OF 1,4-BETA-D-XYLOSIDIC LINKAGES IN XYLANS. A MEMBER OF THE XYLAN ...CATALYSES THE ENDOHYDROL |
Sequence details | CBM6 IS A FRAGMENT OF THIS SEQUENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 20% PEG 1000, 0.2 M SODIUM ACETATE, 0.1 M ACETATE BUFFER PH4.6, 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Date: Mar 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→52 Å / Num. obs: 13033 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 9.1 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 9.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GMM Resolution: 1.6→51.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.71 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107 / 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: 13.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→51.99 Å
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Refine LS restraints |
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