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Yorodumi- PDB-5oht: A GH31 family sulfoquinovosidase from E. coli in complex with aza... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oht | ||||||
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Title | A GH31 family sulfoquinovosidase from E. coli in complex with aza-sugar inhibitor IFGSQ | ||||||
Components | Sulfoquinovosidase | ||||||
Keywords | HYDROLASE / sulfoglycosidase / sulfoglycolysis / complex / general acid-base varient | ||||||
Function / homology | Function and homology information sulfoquinovosidase / sulfoquinovosidase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Jin, Y. / Williams, S.J. / Goddard-Borger, E. / Davies, G.J. | ||||||
Citation | Journal: ACS Cent Sci / Year: 2018 Title: Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases. Authors: Abayakoon, P. / Jin, Y. / Lingford, J.P. / Petricevic, M. / John, A. / Ryan, E. / Wai-Ying Mui, J. / Pires, D.E.V. / Ascher, D.B. / Davies, G.J. / Goddard-Borger, E.D. / Williams, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oht.cif.gz | 291.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oht.ent.gz | 231.8 KB | Display | PDB format |
PDBx/mmJSON format | 5oht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oht_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 5oht_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 5oht_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 5oht_validation.cif.gz | 75.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/5oht ftp://data.pdbj.org/pub/pdb/validation_reports/oh/5oht | HTTPS FTP |
-Related structure data
Related structure data | 5ohsC 5ohyC 5aeeS 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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2 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 78423.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: yihQ, squQ, b3878, JW3849 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32138, sulfoquinovosidase #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: 2.9 Å3/Da / Density % sol: 57.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25 MG/ML-1 PROTEIN IN 50 MM NAPO4 , PH6.5, AND 250 MM NACL BUFFER IS MIXED WITH EQUAL VOLUME OF PRECIPITANT COMPOSED OF 50-60% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1-0.15 M CACL2, AND 20 DEGREE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→44.62 Å / Num. obs: 140829 / % possible obs: 97.8 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0378 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6956 / CC1/2: 0.622 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5aee Resolution: 1.87→44.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.113 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 117.14 Å2 / Biso mean: 42.6633 Å2 / Biso min: 22.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→44.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.918 Å / Total num. of bins used: 20
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