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Yorodumi- PDB-7lha: Structure of the Exo-L-galactose-6-sulfatase BuS1_11 from Bactero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lha | ||||||
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Title | Structure of the Exo-L-galactose-6-sulfatase BuS1_11 from Bacteroides uniformis | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 7lha.cif.gz | 290.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lha.ent.gz | 186 KB | Display | PDB format |
PDBx/mmJSON format | 7lha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lha_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 7lha_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 7lha_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 7lha_validation.cif.gz | 66.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/7lha ftp://data.pdbj.org/pub/pdb/validation_reports/lh/7lha | HTTPS FTP |
-Related structure data
Related structure data | 7lh6C 7lj2C 7ljjC 7lk7C 7lnpC 2qzuS 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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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: Chemical | #3: Chemical | ChemComp-NI / #4: 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: 2.23 Å3/Da / Density % sol: 44.93 % |
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Crystal grow | Temperature: 291.15 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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9792 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45 Å / Num. obs: 79225 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.053 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 79363 / CC1/2: 0.92 / Rpim(I) all: 0.178 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2qzu Resolution: 1.95→40.6 Å / SU ML: 0.1724 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 16.9413 / 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: 18.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→40.6 Å
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Refine LS restraints |
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LS refinement shell |
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