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Yorodumi- PDB-3wkg: Crystal structure of cellobiose 2-epimerase in complex with gluco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wkg | |||||||||
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Title | Crystal structure of cellobiose 2-epimerase in complex with glucosylmannose | |||||||||
Components | Cellobiose 2-epimerase | |||||||||
Keywords | ISOMERASE / (alpha/alpha)6 barrel fold / Epimerase / Carbohydrate/Sugar Binding / Epimerization | |||||||||
Function / homology | Function and homology information cellobiose epimerase / cellobiose epimerase activity / N-acylglucosamine 2-epimerase activity / sulfoquinovose isomerase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / N-acetylmannosamine metabolic process / N-acetylglucosamine metabolic process / peptidase inhibitor activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Rhodothermus marinus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | |||||||||
Authors | Fujiwara, T. / Saburi, W. / Tanaka, I. / Yao, M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural Insights into the Epimerization of beta-1,4-Linked Oligosaccharides Catalyzed by Cellobiose 2-Epimerase, the Sole Enzyme Epimerizing Non-anomeric Hydroxyl Groups of Unmodified Sugars Authors: Fujiwara, T. / Saburi, W. / Matsui, H. / Mori, H. / Yao, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wkg.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wkg.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wkg ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wkg | HTTPS FTP |
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-Related structure data
Related structure data | 3wkfSC 3wkhC 3wkiC 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: 47459.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodothermus marinus (bacteria) / Strain: JCM9785 / Gene: ce / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F8WRK9, cellobiose epimerase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-mannopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Compound details | ONE LIGAND OF THIS STRUCTURE, 4-O-BETA-D-GLUCOSYL-D-MANNOSE(C12H22O11) IS LOCATED AT 502-503, ...ONE LIGAND OF THIS STRUCTURE, 4-O-BETA-D-GLUCOSYL-D-MANNOSE(C12H22O11) IS LOCATED AT 502-503, CHAINE A (REF. LINK RECORD) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M sodium acetate buffer pH4.5, 1.0M ammonium hydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 24, 2012 |
Radiation | Monochromator: cryocooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→50 Å / Num. obs: 59748 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.47→1.56 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.8 / Num. unique all: 9460 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WKF Resolution: 1.47→39.75 Å / SU ML: 0.14 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→39.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4704→1.4933 Å
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