+Open data
-Basic information
Entry | Database: PDB / ID: 5aeg | |||||||||
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Title | A bacterial protein structure in glycoside hydrolase family 31. | |||||||||
Components | ALPHA-GLUCOSIDASE YIHQ | |||||||||
Keywords | HYDROLASE / GH31 / ALPHA-SULFOQUINOVOSIDASE | |||||||||
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: 1.85 Å | |||||||||
Authors | Jin, Y. / Speciale, G. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D. | |||||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Yihq is a Sulfoquinovosidase that Cleaves Sulfoquinovosyl Diacylglyceride Sulfolipids. Authors: Speciale, G. / Jin, Y. / Davies, G.J. / Williams, S.J. / 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 | 5aeg.cif.gz | 289.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aeg.ent.gz | 232.9 KB | Display | PDB format |
PDBx/mmJSON format | 5aeg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aeg_validation.pdf.gz | 472.3 KB | Display | wwPDB validaton report |
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Full document | 5aeg_full_validation.pdf.gz | 482.7 KB | Display | |
Data in XML | 5aeg_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 5aeg_validation.cif.gz | 78.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aeg ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aeg | HTTPS FTP |
-Related structure data
Related structure data | 5aedSC 5aeeC 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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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 78423.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32138, alpha-glucosidase #5: Sugar | ChemComp-B9D / | |
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-Non-polymers , 4 types, 732 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #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 Å3/Da / Density % sol: 38 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 25 MG ML-1 YIHQ PROTEIN STOCK 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 BIS-TRIS, (PH 6.5) AFTER 3-4 DAYS AT 20 ...Details: 25 MG ML-1 YIHQ PROTEIN STOCK 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 BIS-TRIS, (PH 6.5) AFTER 3-4 DAYS AT 20 DEGREE. THE LIGAND I5F WAS SOAKED INTO THE NATIVE CRYSTAL. |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→49.68 Å / Num. obs: 154198 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 95.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5AED Resolution: 1.85→105.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.877 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 14-17 IN CHAIN A ARE DISORDERED DISORDERED REGIONS WERE NOT MODELED IN.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.762 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→105.45 Å
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Refine LS restraints |
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