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- PDB-6r5n: The crystal structure of Glycoside Hydrolase BglX from P. aerugin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r5n | ||||||
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Title | The crystal structure of Glycoside Hydrolase BglX from P. aeruginosa in complex with 1-deoxynojirimycin | ||||||
![]() | Periplasmic beta-glucosidase | ||||||
![]() | HYDROLASE / Glycoside hydrolase | ||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Batuecas, M.T. / Hermoso, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Catalytic Cycle of Glycoside Hydrolase BglX fromPseudomonas aeruginosaand Its Implications for Biofilm Formation. Authors: Mahasenan, K.V. / Batuecas, M.T. / De Benedetti, S. / Kim, C. / Rana, N. / Lee, M. / Hesek, D. / Fisher, J.F. / Sanz-Aparicio, J. / 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 | ![]() | 321 KB | Display | ![]() |
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PDB format | ![]() | 253.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.7 KB | Display | ![]() |
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Full document | ![]() | 461.2 KB | Display | |
Data in XML | ![]() | 61.9 KB | Display | |
Data in CIF | ![]() | 94.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r5iC ![]() 6r5oC ![]() 6r5pC ![]() 6r5rC ![]() 6r5tC ![]() 6r5uC ![]() 6r5vC ![]() 5tf0S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 32 - 764 / Label seq-ID: 1 - 733
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Components
#1: Protein | Mass: 80155.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: bglX, PA1726 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 50 mM Bis Tris, pH 6.5, 30% pentaerythritol ethoxylate and 50 mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2→86.88 Å / Num. obs: 109537 / % possible obs: 97.2 % / Redundancy: 8.9 % / Rpim(I) all: 0.11 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 5282 / Rpim(I) all: 0.58 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TF0 Resolution: 2→81.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.256 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.14 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.568 Å2
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Refinement step | Cycle: 1 / Resolution: 2→81.99 Å
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Refine LS restraints |
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