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- PDB-3gsm: Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Va... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gsm | ||||||
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Title | Vibrio cholerae family 3 glycoside hydrolase (NagZ) bound to N-Valeryl-PUGNAc | ||||||
![]() | Beta-hexosaminidase | ||||||
![]() | HYDROLASE / glycoside hydrolases / Cell cycle / Cell division / Cell shape / Cell wall biogenesis/degradation / Glycosidase / Peptidoglycan synthesis | ||||||
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 | ![]() ![]() | ||||||
![]() | Balcewich, M.D. / Mark, B.L. | ||||||
![]() | ![]() Title: Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ. Authors: Balcewich, M.D. / Stubbs, K.A. / He, Y. / James, T.W. / Davies, G.J. / Vocadlo, D.J. / Mark, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.4 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.6 KB | Display | ![]() |
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Full document | ![]() | 760.3 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wcaC ![]() 3gs6C ![]() 2oxnS 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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Unit cell |
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Details | one biological molecule in the asymmetric unit |
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Components
#1: Protein | Mass: 37714.848 Da / Num. of mol.: 1 / Mutation: E19A, Q22A, K54A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-VPU / [[( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 13% PEG 20,000, 10% glycerol, 100mM Bis-Tris pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→61.08 Å / Num. all: 14609 / Num. obs: 14482 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.97 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OXN Resolution: 2.4→61.08 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 9.329 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.485 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The VPU residue, bound inhibitor N-valeryl PUGNAc, has missing atoms: OAQ CAP OAR NAO CAS CAT CAU CAV CAW CAX. 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.499 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→61.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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