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- PDB-4azi: 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: 4azi | ||||||
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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 | ![]() | 204.6 KB | Display | ![]() |
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PDB format | ![]() | 161.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 44.2 KB | Display | |
Data in CIF | ![]() | 68.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4az5C ![]() 4az6C ![]() 4az7C ![]() 4azbC ![]() 4azcC ![]() 4azgC ![]() 4azhC ![]() 2yl5S 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 49869.020 Da / Num. of mol.: 2 / Fragment: CATALYTIC MODULE, RESIDUES 627-1064 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1162 molecules ![](data/chem/img/OAN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-BR / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, GLY 913 TO TRP ENGINEERED RESIDUE IN CHAIN A, GLY 914 TO TYR ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.95 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→57.1 Å / Num. obs: 68111 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.2 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YL5 Resolution: 1.98→43.47 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.846 / SU B: 5.451 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.214 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.824 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→43.47 Å
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Refine LS restraints |
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