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- PDB-4az5: Differential inhibition of the tandem GH20 catalytic modules in t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4az5 | ||||||
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Title | Differential inhibition of the tandem GH20 catalytic modules in the pneumococcal exo-beta-D-N-acetylglucosaminidase, StrH | ||||||
![]() | BETA-N-ACETYLHEXOSAMINIDASE | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pluvinage, B. / Stubbs, K.A. / Vocadlo, D.J. / Boraston, A.B. | ||||||
![]() | ![]() Title: Inhibition of the Family 20 Glycoside Hydrolase Catalytic Modules in the Streptococcus Pneumoniae Exo-Beta-D-N-Acetylglucosaminidase, Strh. Authors: Pluvinage, B. / Stubbs, K.A. / Vocadlo, D.J. / Boraston, A.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.5 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764.1 KB | Display | ![]() |
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Full document | ![]() | 766.4 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4az6C ![]() 4az7C ![]() 4azbC ![]() 4azcC ![]() 4azgC ![]() 4azhC ![]() 4aziC ![]() 2yl6S S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48207.746 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 181-614 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 681 molecules ![](data/chem/img/NGW.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NGW / ( | ||||||
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#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PE4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→21.99 Å / Num. obs: 49487 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.73→1.82 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YL6 Resolution: 1.73→78.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.814 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.089 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→78.57 Å
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Refine LS restraints |
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