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- PDB-5ly7: Crystal structure of NagZ H174A mutant from Pseudomonas aeruginos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ly7 | ||||||
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Title | Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin | ||||||
![]() | Beta-hexosaminidase | ||||||
![]() | GENE REGULATION / Cell-Wall Recycling Beta-hexosaminidase Pseudomonas aeruginosa Inhibitor | ||||||
Function / homology | ![]() beta-N-acetylhexosaminidase activity / peptidoglycan turnover / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / 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 | ![]() | 137.4 KB | Display | ![]() |
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PDB format | ![]() | 106.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5g1mC ![]() 5g2mC ![]() 5g3rC ![]() 5g5kC ![]() 5g5uC ![]() 5g6tC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: -1 - 332 / Label seq-ID: 20 - 352
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Components
#1: Protein | Mass: 38250.605 Da / Num. of mol.: 2 / Mutation: H174A Source method: isolated from a genetically manipulated source Details: There is a single-point mutation at His174, H174A / Source: (gene. exp.) ![]() ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: nagZ, PA3005 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / 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 |
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: 3.1→73.23 Å / Num. obs: 10753 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 19.14 Å2 / CC1/2: 0.929 / Rmerge(I) obs: 0.182 / Rsym value: 0.146 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.75 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Crystallographic structure of NagZ from Pseudomonas aeruginosa Resolution: 3.1→73.23 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.819 / SU B: 31.324 / SU ML: 0.542 / Cross valid method: THROUGHOUT / ESU R Free: 0.67 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 17.773 Å2
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Refinement step | Cycle: 1 / Resolution: 3.1→73.23 Å
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Refine LS restraints |
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