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- PDB-5utr: Crystal structure of Burkholderia cenocepacia family 3 glycoside ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5utr | ||||||
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Title | Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-butyryl-4,5,6-trihydroxyazepane | ||||||
![]() | Beta-hexosaminidase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Glycoside hydrolase / family 3 / NagZ / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vadlamani, G. / Mark, B.L. | ||||||
![]() | ![]() Title: Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance. Authors: Vadlamani, G. / Stubbs, K.A. / Desire, J. / Bleriot, Y. / 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 | ![]() | 265.6 KB | Display | ![]() |
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PDB format | ![]() | 214.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5utpC ![]() 5utqC ![]() 4g6cS 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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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | Mass: 38116.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A125HFC0, UniProt: B4EA43*PLUS, beta-N-acetylhexosaminidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30-32% PEG8000, 0.1M MES pH 6.2-6.8 / PH range: 6.2-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→66.93 Å / Num. obs: 30692 / % possible obs: 100 % / Redundancy: 3.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2532 / CC1/2: 0.889 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4G6C Resolution: 2.15→66.93 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→66.93 Å
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Refine LS restraints |
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LS refinement shell |
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