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Yorodumi- PDB-6pnr: A GH31 family sulfoquinovosidase from E. rectale in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pnr | ||||||
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Title | A GH31 family sulfoquinovosidase from E. rectale in complex with aza-sugar inhibitor IFGSQ | ||||||
Components | Alpha-glucosidase | ||||||
Keywords | Hydrolase/Hydrolas Inhibitor / Sulfoquinovosidase / sulfolipid / Hydrolase-Hydrolas Inhibitor complex | ||||||
Function / homology | Function and homology information alpha-glucosidase / : / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | [Eubacterium] rectale (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Jarva, M.A. / Lingford, J.P. / John, A. / Goddard-Borger, E.D. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: A GH31 family sulfoquinovosidase from E. rectale in complex with aza-sugar inhibitor IFGSQ Authors: Lingford, J.P. / Jarva, M.A. / John, A. / Goddard-Borger, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pnr.cif.gz | 298.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pnr.ent.gz | 237.9 KB | Display | PDB format |
PDBx/mmJSON format | 6pnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pnr_validation.pdf.gz | 370 KB | Display | wwPDB validaton report |
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Full document | 6pnr_full_validation.pdf.gz | 370 KB | Display | |
Data in XML | 6pnr_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 6pnr_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/6pnr ftp://data.pdbj.org/pub/pdb/validation_reports/pn/6pnr | HTTPS FTP |
-Related structure data
Related structure data | 5aedS S: Starting model for refinement |
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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: 78882.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) [Eubacterium] rectale (bacteria) / Gene: DW001_07735, DW028_04245, DW967_02630 / Production host: Escherichia coli (E. coli) References: UniProt: A0A396FTG2, UniProt: C4ZGB7*PLUS, alpha-glucosidase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 15% PEG 4000, 0.1 M MgCl2, 0.05 M Tris-HCl, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9573 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9573 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→49.36 Å / Num. obs: 126226 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 33.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.043 / Rrim(I) all: 0.1 / Net I/σ(I): 10.3 / Num. measured all: 663655 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AED Resolution: 1.9→47.56 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.86 Å2 / Biso mean: 36.8466 Å2 / Biso min: 20.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→47.56 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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