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- PDB-3suw: Crystal structure of beta-hexosaminidase from Paenibacillus sp. T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3suw | ||||||
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Title | Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with NHAc-CAS | ||||||
![]() | Beta-hexosaminidase | ||||||
![]() | HYDROLASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Tim barrel / Carbohydrate/Sugar Binding | ||||||
Function / homology | ![]() glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate binding / carbohydrate metabolic process / lysosome / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sumida, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Gaining insight into the inhibition of glycoside hydrolase family 20 exo-beta-N-acetylhexosaminidases using a structural approach Authors: Sumida, T. / Stubbs, K.A. / Ito, M. / Yokoyama, 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 | ![]() | 224.7 KB | Display | ![]() |
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PDB format | ![]() | 176.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.7 KB | Display | ![]() |
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Full document | ![]() | 468.2 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 39.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3surC ![]() 3susC ![]() 3sutC ![]() 3suuC ![]() 3suvC ![]() 3gh4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 57566.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D0VX21, UniProt: D2KW09*PLUS, beta-N-acetylhexosaminidase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GC2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Na-citrate, PEG 2000, (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 41771 / Redundancy: 7.1 % / Rsym value: 0.178 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.4 % / Rsym value: 0.648 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GH4 Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.523 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 13.275 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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