[English] 日本語
Yorodumi- PDB-6gn6: Alpha-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gn6 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Alpha-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus | ||||||||||||
Components | Alpha-L-fucosidase | ||||||||||||
Keywords | HYDROLASE / Alpha-L-fucosidase / GH29 / active site complementation / hexamer | ||||||||||||
Function / homology | Function and homology information alpha-L-fucosidase / alpha-L-fucosidase activity / fucose metabolic process Similarity search - Function | ||||||||||||
Biological species | Paenibacillus thiaminolyticus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Kovalova, T. / Koval, T. / Lipovova, P. / Dohnalek, J. | ||||||||||||
Funding support | Czech Republic, 3items
| ||||||||||||
Citation | Journal: Glycobiology / Year: 2019 Title: Active site complementation and hexameric arrangement in the GH family 29; a structure-function study of alpha-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus. Authors: Kovalova, T. / Koval, T. / Benesova, E. / Vodickova, P. / Spiwok, V. / Lipovova, P. / Dohnalek, J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6gn6.cif.gz | 546.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6gn6.ent.gz | 448.6 KB | Display | PDB format |
PDBx/mmJSON format | 6gn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gn6_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6gn6_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 6gn6_validation.xml.gz | 104.5 KB | Display | |
Data in CIF | 6gn6_validation.cif.gz | 148.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/6gn6 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/6gn6 | HTTPS FTP |
-Related structure data
Related structure data | 2wvsS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 51249.449 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus thiaminolyticus (bacteria) Gene: aLfuk1 / Plasmid: pET16b-alphaLF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E3PQQ9, alpha-L-fucosidase |
---|
-Sugars , 2 types, 14 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #3: Sugar | ChemComp-GLC / |
---|
-Non-polymers , 7 types, 1411 molecules
#4: Chemical | ChemComp-PGE / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PG4 / | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.7 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% (w/v) PEG 3350, 0.2 M Ammonium acetate, 0.1 M BIS-TRIS buffer, Additive: 50 mM Maltose |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.93 Å / Num. obs: 157780 / % possible obs: 99.4 % / Observed criterion σ(I): -3.7 / Redundancy: 5 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WVS Resolution: 2.2→48.93 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 6.104 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.214 Stereochemistry target values: THE STEREOCHEMISTRY LIBRARY OF CCP4 VERSION 7.0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LAST REFINEMENT CYCLE WAS PERFORMED AGAINST ALL REFLECTIONS OF THE DATA SET.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.97 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|