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Yorodumi- PDB-6r5i: The crystal structure of the Glycoside Hydrolase BglX from P. aer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r5i | ||||||
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Title | The crystal structure of the Glycoside Hydrolase BglX from P. aeruginosa | ||||||
Components | Periplasmic beta-glucosidase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase | ||||||
Function / homology | Function and homology information glucan catabolic process / beta-glucosidase / beta-glucosidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 6r5i.cif.gz | 313.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r5i.ent.gz | 247.8 KB | Display | PDB format |
PDBx/mmJSON format | 6r5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r5i_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 6r5i_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 6r5i_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 6r5i_validation.cif.gz | 89.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/6r5i ftp://data.pdbj.org/pub/pdb/validation_reports/r5/6r5i | HTTPS FTP |
-Related structure data
Related structure data | 6r5nC 6r5oC 6r5pC 6r5rC 6r5tC 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: _ / 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.) 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 Variant: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Production host: Escherichia coli (E. coli) / References: UniProt: Q9I311 #2: Chemical | #3: Chemical | #4: 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: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50mM BIS TRIS pH6.5 + 30% pentaerythritol ethoxylate + 50mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97927 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.57 Å / Num. obs: 124434 / % possible obs: 96.2 % / Redundancy: 2.4 % / Rpim(I) all: 0.1 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 6074 / Rpim(I) all: 0.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TF0 Resolution: 1.8→19.93 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.994 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.131 / 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: 17.327 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.93 Å
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Refine LS restraints |
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