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Yorodumi- PDB-1w8t: CBM29-2 mutant K74A complexed with cellulohexaose: Probing the Me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w8t | |||||||||
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Title | CBM29-2 mutant K74A complexed with cellulohexaose: Probing the Mechanism of Ligand Recognition by Family 29 Carbohydrate Binding Modules | |||||||||
Components | NON CATALYTIC PROTEIN 1 | |||||||||
Keywords | CARBOHYDRATE-BINDING DOMAIN / CARBOHYDRATE BINDING MODULE / GLUCOMANNAN / CELLOHEXAOSE / MANNOHEXAOSE / CELLULOSOME | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | PIROMYCES EQUI (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Flint, J. / Bolam, D.N. / Nurizzo, D. / Taylor, E.J. / Williamson, M.P. / Walters, C. / Davies, G.J. / Gilbert, H.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Probing the Mechanism of Ligand Recognition in Family 29 Carbohydrate-Binding Modules Authors: Flint, J. / Bolam, D.N. / Nurizzo, D. / Taylor, E.J. / Williamson, M.P. / Walters, C. / Davies, G.J. / Gilbert, H.J. | |||||||||
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 | 1w8t.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w8t.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w8t ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w8t | HTTPS FTP |
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-Related structure data
Related structure data | 1w8uC 1w8wC 1w8zC 1w90C 1w9fC 1wcuC 1gwmS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16608.242 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE 2, RESIDUES 334-478 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PIROMYCES EQUI (fungus) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C171 |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Details: 0.18 M AMMONIUM TARTRATE, 18% PEG 3350, 25% MPD, 5% GLYCEROL, 10 MM CELLOHEXAOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 30504 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 12.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GWM Resolution: 1.4→19.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.647 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.057 / 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: 13.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19.28 Å
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Refine LS restraints |
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