+Open data
-Basic information
Entry | Database: PDB / ID: 5mum | ||||||
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Title | Glycoside Hydrolase BACINT_00347 | ||||||
Components | BACINT_00347 | ||||||
Keywords | HYDROLASE / Rhamnosidase / Bacteroides / Beta-propeller | ||||||
Function / homology | Sialidase superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Bacteroides intestinalis DSM 17393 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Henrissat, B. / Gilbert, H.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Unusual active site location and catalytic apparatus in a glycoside hydrolase family. Authors: Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Henrissat, B. / Gilbert, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mum.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mum.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/5mum ftp://data.pdbj.org/pub/pdb/validation_reports/mu/5mum | HTTPS FTP |
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-Related structure data
Related structure data | 5mukC 5mulC 5mvhC 4irtS 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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-Components
#1: Protein | Mass: 49838.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides intestinalis DSM 17393 (bacteria) Gene: BACINT_00347 / Production host: Escherichia coli (E. coli) / References: UniProt: B3C613 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 and 200 mM Tri-potassium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→68.6 Å / Num. obs: 255841 / % possible obs: 98.4 % / Redundancy: 3.3 % / Net I/σ(I): 12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IRT Resolution: 1.8→68.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.495 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / 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: 13.636 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→68.6 Å
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Refine LS restraints |
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