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- PDB-8hvd: 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: 8hvd | ||||||
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Title | Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, galacto-N-biose complex 2 | ||||||
![]() | Lacto-N-biosidase | ||||||
![]() | HYDROLASE / Glycoside hydrolase / lacto-N-biosidase / galacto-N-biose complex 2 | ||||||
Function / homology | ![]() beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process 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 | ![]() | 149.8 KB | Display | ![]() |
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PDB format | ![]() | 110.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 827.1 KB | Display | ![]() |
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Full document | ![]() | 828.8 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 47.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hvbC ![]() 8hvcC 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: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.25 M Ammonium fluoride, 12.5%(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 PILATUS3 S 2M / Detector: PIXEL / Date: Jun 28, 2022 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, liquid, nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→47.99 Å / Num. obs: 107633 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 10.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.41→1.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16650 / CC1/2: 0.784 / Rpim(I) all: 0.324 / Rrim(I) all: 0.583 / % 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: 14.688 Å2
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Refinement step | Cycle: 1 / Resolution: 1.41→47.94 Å
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Refine LS restraints |
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