+Open data
-Basic information
Entry | Database: PDB / ID: 3wkf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of cellobiose 2-epimerase | ||||||
Components | Cellobiose 2-epimeraseCellobiose epimerase | ||||||
Keywords | ISOMERASE / (alpha/alpha)6 barrel fold / Epimerase / Carbohydrate/Sugar Binding / Epimerization | ||||||
Function / homology | Function and homology information cellobiose epimerase / cellobiose epimerase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Rhodothermus marinus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.743 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wkf.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wkf.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wkf ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wkf | HTTPS FTP |
---|
-Related structure data
Related structure data | 3wkgC 3wkhC 3wkiC 3vw5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.31 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2012 |
Radiation | Monochromator: the rotated-inclined double-crystal monochrometer Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. obs: 36127 / % possible obs: 99.9 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.74→1.81 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4 / Num. unique all: 3531 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VW5 Resolution: 1.743→32.022 Å / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.25 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.743→32.022 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.743→1.7899 Å
|