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Yorodumi- PDB-6tvk: Alpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tvk | ||||||||||||||||||
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Title | Alpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus | ||||||||||||||||||
Components | Alpha-L-fucosidase | ||||||||||||||||||
Keywords | HYDROLASE / ALPHA-L-FUCOSIDASE / GH151 / ACTIVE SITE COMPLEMENTATION / TETRAMER | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Paenibacillus thiaminolyticus (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||||||||||||||
Authors | Kovalova, T. / Koval, T. / Lipovova, P. / Dohnalek, J. | ||||||||||||||||||
Funding support | Czech Republic, 5items
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Citation | Journal: Febs J. / Year: 2022 Title: The first structure-function study of GH151 alpha-l-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity Authors: Koval'ova, T. / Koval, T. / Stransky, J. / Kolenko, P. / Duskova, J. / Svecova, L. / Vodickova, P. / Spiwok, V. / Benesova, E. / Lipovova, P. / Dohnalek, J. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tvk.cif.gz | 157.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tvk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/6tvk ftp://data.pdbj.org/pub/pdb/validation_reports/tv/6tvk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 77843.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residue Cys488 is oxidized Source: (gene. exp.) Paenibacillus thiaminolyticus (bacteria) Gene: aLfuk2, NCTC11027_00201 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K0JCW6 |
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-Non-polymers , 5 types, 363 molecules
#2: Chemical | ChemComp-TBR / | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.41 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Condition: 0.1 M NaCl, 1.5 M ammonium acetate, 0.1 M BIS-TRIS pH 6.5 The condition was diluted to 80% 5 mM maltose as an additive |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.08 Å / Num. obs: 63022 / % possible obs: 99.7 % / Redundancy: 40.1 % / Biso Wilson estimate: 43.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.031 / Rrim(I) all: 0.144 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 42.3 % / Rmerge(I) obs: 3.57 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4375 / CC1/2: 0.822 / Rpim(I) all: 0.77 / Rrim(I) all: 3.653 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→49.08 Å / Cor.coef. Fo:Fc: 0.966 / SU B: 4.623 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Hydrogens have been added in their riding positions. The final refinement cycle was performed against all measured intensities.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.086 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→49.08 Å
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Refine LS restraints |
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LS refinement shell |
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