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Open data
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Basic information
Entry | Database: PDB / ID: 3vw5 | ||||||
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Title | Crystal structure of sugar epimerase from ruminal bacterium | ||||||
![]() | Cellobiose 2-epimerase | ||||||
![]() | ISOMERASE / (alpha/alpha)6 barrel fold / Epimerase / Carbohydrate/Sugar Binding / Epimerization | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujiwara, T. / Saburi, W. / Tanaka, I. / Yao, M. | ||||||
![]() | ![]() Title: Crystal structure of Ruminococcus albus cellobiose 2-epimerase: structural insights into epimerization of unmodified sugar Authors: Fujiwara, T. / Saburi, W. / Inoue, S. / Mori, H. / Matsui, H. / Tanaka, I. / Yao, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.1 KB | Display | ![]() |
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PDB format | ![]() | 195.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.7 KB | Display | ![]() |
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Full document | ![]() | 471.6 KB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 58.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gt5S 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45362.727 Da / Num. of mol.: 3 / Mutation: G38E, P138L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A8CF79, UniProt: P0DKY4*PLUS, cellobiose epimerase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.6M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: mirrors |
Radiation | Monochromator: the rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45 Å / Num. obs: 57248 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 48.981 Å2 / Rmerge(I) obs: 0.0085 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8838 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GT5 Resolution: 2.6→39.127 Å / SU ML: 0.63 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Phase error: 21.82
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.384 Å2 / ksol: 0.427 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 4.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→39.127 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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