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- PDB-6r5v: The crystal structure of Glycoside Hydrolase BglX inactive mutant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r5v | |||||||||
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Title | The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with xylotriose | |||||||||
![]() | 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 | ![]() | 320.3 KB | Display | ![]() |
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PDB format | ![]() | 252.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6r5iC ![]() 6r5nC ![]() 6r5oC ![]() 6r5pC ![]() 6r5rC ![]() 6r5tC ![]() 6r5uC ![]() 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
-Protein / Sugars , 2 types, 4 molecules BA
#1: Protein | Mass: 80154.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: bglX, PA1726 / Production host: ![]() ![]() #2: Polysaccharide | |
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-Non-polymers , 4 types, 1027 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PGE / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis Tris, pH 5.5, 17% PEG 10000 and 100 mM ammonium acetate |
-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: Sep 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979257 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.27 Å / Num. obs: 123955 / % possible obs: 96.3 % / Redundancy: 3 % / Rpim(I) all: 0.08 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 6063 / Rpim(I) all: 0.42 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TF0 Resolution: 1.8→45.27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.748 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.119 / 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: 19.184 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→45.27 Å
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Refine LS restraints |
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