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Yorodumi- PDB-7lj2: Structure of Exo-L-galactose-6-sulfatase BuS1_11 from Bacteroides... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lj2 | ||||||
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Title | Structure of Exo-L-galactose-6-sulfatase BuS1_11 from Bacteroides uniformis in complex with neoporphyrabiose | ||||||
Components | Exo-L-galactose-6-sulfatase | ||||||
Keywords | HYDROLASE / sulfatase / porphyran / carbohydrate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides uniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Robb, C.S. / Boraston, A.B. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Metabolism of a hybrid algal galactan by members of the human gut microbiome. Authors: Robb, C.S. / Hobbs, J.K. / Pluvinage, B. / Reintjes, G. / Klassen, L. / Monteith, S. / Giljan, G. / Amundsen, C. / Vickers, C. / Hettle, A.G. / Hills, R. / Xing, X. / Montina, T. / Zandberg, ...Authors: Robb, C.S. / Hobbs, J.K. / Pluvinage, B. / Reintjes, G. / Klassen, L. / Monteith, S. / Giljan, G. / Amundsen, C. / Vickers, C. / Hettle, A.G. / Hills, R. / Xing, X. / Montina, T. / Zandberg, W.F. / Abbott, D.W. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lj2.cif.gz | 283.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lj2.ent.gz | 182.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lj2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7lj2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7lj2_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 7lj2_validation.cif.gz | 59.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/7lj2 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/7lj2 | HTTPS FTP |
-Related structure data
Related structure data | 7lh6C 7lhaSC 7ljjC 7lk7C 7lnpC 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
#1: Protein | Mass: 62254.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: Bun01g_38470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y1VMZ7 #2: Polysaccharide | Type: oligosaccharide / Mass: 422.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 7.5), 0.2 M MgCl2, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 42974 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 39.08 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.063 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.492 / Num. unique obs: 4494 / CC1/2: 0.729 / Rpim(I) all: 0.313 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LHA Resolution: 2.4→29.79 Å / SU ML: 0.341 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1967 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.79 Å
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Refine LS restraints |
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LS refinement shell |
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