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- PDB-6mvf: Crystal structure of FMN-binding beta-glucuronidase from Facaelib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mvf | ||||||
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Title | Crystal structure of FMN-binding beta-glucuronidase from Facaelibacterium prausnitzii L2-6 | ||||||
![]() | Beta-galactosidase/beta-glucuronidase | ||||||
![]() | HYDROLASE / glycoside hydrolase / FMN / beta-glucuronidase | ||||||
Function / homology | ![]() beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pellock, S.J. / Redinbo, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and Characterization of FMN-Binding beta-Glucuronidases in the Human Gut Microbiome. Authors: Pellock, S.J. / Walton, W.G. / Ervin, S.M. / Torres-Rivera, D. / Creekmore, B.C. / Bergan, G. / Dunn, Z.D. / Li, B. / Tripathy, A. / Redinbo, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 783 KB | Display | ![]() |
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PDB format | ![]() | 637.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 142.1 KB | Display | |
Data in CIF | ![]() | 200.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mvgC ![]() 6mvhC ![]() 3cmgS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 86281.453 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: FP2_04120 / Production host: ![]() ![]() #2: Chemical | ChemComp-FMN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 11.1 mg/mL protein, 0.2 M magnesium chloride, 10% w/v PEG 3000, 0.1 M sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→29.52 Å / Num. obs: 163078 / % possible obs: 99.58 % / Redundancy: 5 % / Rmerge(I) obs: 0.1212 / Net I/σ(I): 11.22 |
Reflection shell | Resolution: 2.55→2.641 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5703 / Mean I/σ(I) obs: 2.58 / Num. unique obs: 16164 / % possible all: 99.53 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CMG Resolution: 2.55→29.524 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.48 / 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: 2.55→29.524 Å
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Refine LS restraints |
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LS refinement shell |
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