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Yorodumi- PDB-3acg: Crystal Structure of Carbohydrate-Binding Module Family 28 from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3acg | |||||||||
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Title | Crystal Structure of Carbohydrate-Binding Module Family 28 from Clostridium josui Cel5A in complex with cellobiose | |||||||||
Components | Beta-1,4-endoglucanase | |||||||||
Keywords | HYDROLASE / beta-jellyroll / cellulose-binding domain | |||||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridium josui (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Tsukimoto, K. / Takada, R. / Araki, Y. / Suzuki, K. / Karita, S. / Wakagi, T. / Shoun, H. / Watanabe, T. / Fushinobu, S. | |||||||||
Citation | Journal: Febs Lett. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3acg.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3acg.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 3acg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/3acg ftp://data.pdbj.org/pub/pdb/validation_reports/ac/3acg | HTTPS FTP |
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-Related structure data
Related structure data | 3acfC 3achC 3aciC 1uwwS 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
-Protein / Sugars , 2 types, 2 molecules A
#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.) Clostridium josui (bacteria) / Gene: celA / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q59290, cellulase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose |
-Non-polymers , 4 types, 417 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #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: 2.12 Å3/Da / Density % sol: 42.03 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 31189 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.08 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.376 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UWW Resolution: 1.5→27.27 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.082 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.074 / 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: 54.16 Å2 / Biso mean: 18.44 Å2 / Biso min: 8.11 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→27.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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