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- PDB-5g6t: Crystal structure of Zn-containing NagZ H174A mutant from Pseudom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g6t | ||||||
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Title | Crystal structure of Zn-containing NagZ H174A mutant from Pseudomonas aeruginosa | ||||||
![]() | BETA-HEXOSAMINIDASE | ||||||
![]() | HYDROLASE / CELL-WALL RECYCLING / ANTIBIOTIC RESISTANCE / GLYCOSIDE HYDROLASE / N-ACETYLGLUCOSAMINIDASE / BETA-HEXOSAMINIDASE / PEPTIDOGLYCAN | ||||||
Function / homology | ![]() beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division ...beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / response to antibiotic / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Acebron, I. / Artola-Recolons, C. / Mahasenan, K. / Mobashery, S. / Hermoso, J.A. | ||||||
![]() | ![]() Title: Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa. Authors: Acebron, I. / Mahasenan, K.V. / De Benedetti, S. / Lee, M. / Artola-Recolons, C. / Hesek, D. / Wang, H. / Hermoso, J.A. / Mobashery, 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 | ![]() | 264 KB | Display | ![]() |
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PDB format | ![]() | 214.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.1 KB | Display | ![]() |
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Full document | ![]() | 467.1 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g1mC ![]() 5g2mC ![]() 5g3rC ![]() 5g5kC ![]() 5g5uC ![]() 5ly7C 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
#1: Protein | Mass: 38250.605 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: BOTH PROTEIN CHAINS CONTAIN A HIS RESIDUE AT POSITION -1 FROM THE FUSION TAG USED FOR PURIFICATION. THE SEQUENCE INCLUDES THE SINGLE-POINT MUTATION H174A THAT MAKES THIS PROTEIN INACTIVE. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Nonpolymer details | ZINC ION (ZN): THE SOURCE OF ZN IS UNKNOWN. IT IS LIKELY THAT ZN COMES EITHER THE EXPRESSION HOST ...ZINC ION (ZN): THE SOURCE OF ZN IS UNKNOWN. IT IS LIKELY THAT ZN COMES EITHER THE EXPRESSION | Sequence details | THE EXPERIMENT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.8 % / Description: NONE |
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Crystal grow | pH: 6 Details: 30% PEG 8000 100 MM SODIUM CACODYLATE PH 6.0 200 MM SODIUM ACETATE PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2015 / Details: KB MIRRORS |
Radiation | Monochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→47.68 Å / Num. obs: 36891 / % possible obs: 97.2 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Biso Wilson estimate: 24.01 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.6 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: APO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA Resolution: 2.15→44.937 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 24.87 / Stereochemistry target values: ML Details: RESIDUES 124-135 AND 171-174 IN CHAIN A, AND REIDUES 124-134, 171-175 AND 249-251 IN CHAIN B WERE NOT MODELED DUE TO POOR ELECTRON DENSITY.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→44.937 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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