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- PDB-5g3r: Crystal structure of NagZ from Pseudomonas aeruginosa in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g3r | ||||||
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Title | Crystal structure of NagZ from Pseudomonas aeruginosa in complex with N-acetylglucosamine and L-Ala-1,6-anhydroMurNAc | ||||||
![]() | 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 | ![]() | 274.8 KB | Display | ![]() |
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PDB format | ![]() | 224.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.5 KB | Display | ![]() |
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Full document | ![]() | 1017.3 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g1mC ![]() 5g2mC ![]() 5g5kC ![]() 5g5uC ![]() 5g6tC ![]() 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: 38317.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CHAIN A CONTAINS A SMALL FRAGMENT (GSH) FROM THE FUSION TAG USED FOR PURIFICATION, AND CHAIN B CONTAINS ONLY A HIS RESIDUE AT POSITION -1 FROM THE SAME FUSION TAG Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | L-ALA-1,6-ANHYDRO-N-ACETYLMURAMIC ACID (89A): THIS MOLECULES IS ONE OF THE PRODUCTS GENERATED BY ...L-ALA-1,6-ANHYDRO-N-ACETYLMURA | Sequence details | THE SEQUENCE CONTAINS A HIS-TAG AT THE N-TERMINUS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.4 % / 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 1, 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: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→47.8 Å / Num. obs: 36231 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 34.64 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.18→2.25 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: APO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA Resolution: 2.18→47.804 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.86 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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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: 46.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→47.804 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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