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- PDB-7byu: Crystal structure of Acidovorax avenae L-fucose mutarotase (apo form) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7byu | ||||||
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Title | Crystal structure of Acidovorax avenae L-fucose mutarotase (apo form) | ||||||
![]() | L-fucose mutarotase | ||||||
![]() | SUGAR BINDING PROTEIN / L-fucose / Mutarotase | ||||||
Function / homology | Rhamnose/fucose mutarotase / L-rhamnose mutarotase / racemase and epimerase activity, acting on carbohydrates and derivatives / Dimeric alpha-beta barrel / Chem-1PG / L-rhamnose mutarotase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watanabe, Y. / Fukui, Y. / Watanabe, S. | ||||||
![]() | ![]() Title: Functional and structural characterization of a novel L-fucose mutarotase involved in non-phosphorylative pathway of L-fucose metabolism. Authors: Watanabe, Y. / Watanabe, S. / Fukui, Y. / Nishiwaki, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.6 KB | Display | ![]() |
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PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 961.2 KB | Display | ![]() |
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Full document | ![]() | 963 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bywC ![]() 1x8dS S: Starting model for refinement C: citing same article ( |
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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: 14143.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 19860 / Gene: Acav_1655 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.8 M potassium sodium tartrate, 0.1 M Tris-HCl pH 8.5, 0.5% PEGMME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 18794 / % possible obs: 99.7 % / Redundancy: 5.2 % / CC1/2: 0.996 / Rpim(I) all: 0.037 / Rrim(I) all: 0.085 / Rsym value: 0.076 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.21→2.27 Å / Redundancy: 2.58 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1637 / CC1/2: 0.756 / Rpim(I) all: 0.372 / Rrim(I) all: 0.843 / Rsym value: 0.755 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1X8D Resolution: 2.206→45.415 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 29.59 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.5 Å2 / Biso mean: 61.1032 Å2 / Biso min: 31.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.206→45.415 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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