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- PDB-3suu: 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: 3suu | ||||||
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Title | Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with Gal-PUGNAc | ||||||
![]() | Beta-hexosaminidase![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() ![]() | ||||||
Function / homology | ![]() glycosaminoglycan metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 231.5 KB | Display | ![]() |
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PDB format | ![]() | 181.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3surC ![]() 3susC ![]() 3sutC ![]() 3suvC ![]() 3suwC ![]() 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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1 |
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Unit cell |
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Components on special symmetry positions |
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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, ![]() |
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#2: Chemical | ChemComp-SO4 / ![]() |
#3: Chemical | ChemComp-OGN / [( |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.57 % |
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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 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→50 Å / Num. obs: 70177 / Redundancy: 7.5 % / Rsym value: 0.097 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 7.4 % / Rsym value: 0.374 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3GH4 Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.526 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.073 / 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: 10.779 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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