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Yorodumi- PDB-6r5t: The crystal structure of Glycoside Hydrolase BglX inactive mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r5t | |||||||||
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Title | The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with lactose | |||||||||
Components | Periplasmic beta-glucosidase | |||||||||
Keywords | HYDROLASE / Glycoside hydrolase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Batuecas, M.T. / Hermoso, J.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r5t.cif.gz | 330.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r5t.ent.gz | 261.4 KB | Display | PDB format |
PDBx/mmJSON format | 6r5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/6r5t ftp://data.pdbj.org/pub/pdb/validation_reports/r5/6r5t | HTTPS FTP |
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-Related structure data
Related structure data | 6r5iC 6r5nC 6r5oC 6r5pC 6r5rC 6r5uC 6r5vC 5tf0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / 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: 0 / 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.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: bglX, PA1726 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I311 #2: Polysaccharide | |
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-Non-polymers , 4 types, 1399 molecules
#3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.72 % |
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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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å |
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: 1.6→45.17 Å / Num. obs: 175334 / % possible obs: 96.1 % / Redundancy: 3.3 % / Rpim(I) all: 0.05 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 8534 / Rpim(I) all: 0.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5tf0 Resolution: 1.6→45.17 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.614 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / 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: 20.863 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→45.17 Å
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Refine LS restraints |
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