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Yorodumi- PDB-2v4v: Crystal Structure of a Family 6 Carbohydrate-Binding Module from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v4v | |||||||||
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Title | Crystal Structure of a Family 6 Carbohydrate-Binding Module from Clostridium cellulolyticum in complex with xylose | |||||||||
Components | GH59 GALACTOSIDASE | |||||||||
Keywords | HYDROLASE / FAMILY 6 CARBOHYDRATE BINDING MODULE / CCCBM6 | |||||||||
Function / homology | Function and homology information galactosylceramide catabolic process / galactosylceramidase activity / cellulase / cellulase activity / xylan catabolic process / carbohydrate binding Similarity search - Function | |||||||||
Biological species | CLOSTRIDIUM CELLULOLYTICUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Abbott, D.W. / Ficko-Blean, E. / Lammerts van Bueren, A. / Coutinho, P.M. / Henrissat, B. / Gilbert, H.J. / Boraston, A.B. | |||||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Analysis of the Structural and Functional Diversity of Plant Cell Wall Specific Family 6 Carbohydrate Binding Modules. Authors: Abbott, D.W. / Ficko-Blean, E. / Van Bueren, A.L. / Rogowski, A. / Cartmell, A. / Coutinho, P.M. / Henrissat, B. / 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 | 2v4v.cif.gz | 42.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v4v.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 2v4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/2v4v ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v4v | HTTPS FTP |
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-Related structure data
Related structure data | 1gmmS 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
#1: Protein | Mass: 13724.653 Da / Num. of mol.: 1 / Fragment: CCCBM6, RESIDUES 922-1050 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM CELLULOLYTICUM (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0PRN1 |
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#2: Sugar | ChemComp-XYP / |
#3: Chemical | ChemComp-NA / |
#4: 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: 1.97 Å3/Da / Density % sol: 36.92 % / Description: NONE |
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Crystal grow | Details: 20% PEG 3350, 0.1M NAOAC, 0.1M NACITRATE.2H20 PH 5.8 |
-Data collection
Diffraction | Mean temperature: 113.15 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→93.25 Å / Num. obs: 20980 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.37 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GMM Resolution: 1.5→93.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.436 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.082 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→93.25 Å
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