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- PDB-3ach: Crystal Structure of Carbohydrate-Binding Module Family 28 from C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ach | |||||||||
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Title | Crystal Structure of Carbohydrate-Binding Module Family 28 from Clostridium josui Cel5A in complex with cellotetraose | |||||||||
![]() | Beta-1,4-endoglucanase | |||||||||
![]() | HYDROLASE / beta-jellyroll / cellulose-binding domain | |||||||||
Function / homology | ![]() cellulase / cellulase activity / cellulose catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tsukimoto, K. / Takada, R. / Araki, Y. / Suzuki, K. / Karita, S. / Wakagi, T. / Shoun, H. / Watanabe, T. / Fushinobu, S. | |||||||||
![]() | ![]() Title: Recognition of cellooligosaccharides by a family 28 carbohydrate-binding module. Authors: Tsukimoto, K. / Takada, R. / Araki, Y. / Suzuki, K. / Karita, S. / Wakagi, T. / Shoun, H. / Watanabe, T. / Fushinobu, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.5 KB | Display | ![]() |
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PDB format | ![]() | 43.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 699.2 KB | Display | ![]() |
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Full document | ![]() | 701.6 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3acfC ![]() 3acgC ![]() 3aciC ![]() 1uwwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22390.189 Da / Num. of mol.: 1 / Fragment: UNP residues 560-752 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: PEG 8000, KH2PO4, vapor diffusion, sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 35569 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.047 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.247 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UWW Resolution: 1.4→27.34 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 1 / SU B: 0.894 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 55.44 Å2 / Biso mean: 19.325 Å2 / Biso min: 9.57 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→27.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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