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- PDB-8hvb: Crystal structure of lacto-N-biosidase StrLNBase from Streptomyce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hvb | ||||||
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Title | Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, lacto-N-biose complex | ||||||
![]() | Lacto-N-biosidase![]() | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fushinobu, S. / Yamada, C. / Fujio, N. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of glycoside hydrolase family 20 lacto-N-biosidase from soil bacterium Streptomyces sp. strain 142 Authors: Fujio, N. / Yamada, C. / Fushinobu, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.4 KB | Display | ![]() |
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PDB format | ![]() | 103.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8hvcC ![]() 8hvdC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 66234.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Sugar | ChemComp-GAL / ![]() |
#3: Sugar | ChemComp-NDG / ![]() |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.68 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.3 M Ammonium fluoride, 10%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 21, 2022 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→48.5 Å / Num. obs: 62063 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 12.18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.057 / Rrim(I) all: 0.153 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3045 / CC1/2: 0.913 / Rpim(I) all: 0.391 / Rrim(I) all: 1.049 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.474 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→48.5 Å
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Refine LS restraints |
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