- PDB-6dq3: Streptococcus pyogenes deacetylase PplD in complex with acetate -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6dq3
Title
Streptococcus pyogenes deacetylase PplD in complex with acetate
Components
Polysaccharide deacetylase
Keywords
HYDROLASE / Group A Streptococcus / GAS / Lancefield group A carbohydrate / metalloenzyme / zinc / carbohydrate esterase 4 family / imidazolate / imidazolide
Function / homology
Function and homology information
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / membrane => GO:0016020 / carbohydrate metabolic process Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
THE AUTHORS STATE THAT THE LIGAND IS IMIDAZOLATE, I.E. DEPROTONATED IMIDAZOLE. IN THIS STRUCTURE, ...THE AUTHORS STATE THAT THE LIGAND IS IMIDAZOLATE, I.E. DEPROTONATED IMIDAZOLE. IN THIS STRUCTURE, THE IMIDAZOLATE IS BRIDGING TWO ZN IONS.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.21 Å3/Da / Density % sol: 44.23 % / Description: prism
Method to determine structure: SAD / Resolution: 1.78→39.694 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 26.4 / Stereochemistry target values: ML / Details: Low occupancy Zn ions have not been modeled
Rfactor
Num. reflection
% reflection
Rfree
0.2164
4297
5.11 %
Rwork
0.1797
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obs
0.1816
84025
99.17 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL