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Yorodumi- PDB-7lnp: Structure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lnp | ||||||
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Title | Structure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) from Bacteroides plebeius in complex with paranitrophenyl-alpha-L-galactopyranoside | ||||||
Components | Exo-alpha-L-galactosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase / porphyran / carbohydrate | ||||||
Function / homology | Function and homology information alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / metal ion binding Similarity search - Function | ||||||
Biological species | Bacteroides plebeius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Boraston, A.B. / Robb, C.S. | ||||||
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 | 7lnp.cif.gz | 568.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lnp.ent.gz | 369.8 KB | Display | PDB format |
PDBx/mmJSON format | 7lnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lnp_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7lnp_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7lnp_validation.xml.gz | 81 KB | Display | |
Data in CIF | 7lnp_validation.cif.gz | 110.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/7lnp ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lnp | HTTPS FTP |
-Related structure data
Related structure data | 7lh6C 7lhaC 7lj2C 7ljjSC 7lk7C 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ACDE
#1: Protein | Mass: 68349.344 Da / Num. of mol.: 4 / Mutation: D264N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides plebeius (bacteria) / Strain: DSM 17135 / JCM 12973 / M2 / Gene: BACPLE_01702 / Production host: Escherichia coli (E. coli) / References: UniProt: B5CYA5 |
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-Non-polymers , 6 types, 707 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-Y9Y / #4: Chemical | ChemComp-NI / #5: Chemical | ChemComp-NA / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M BIS-TRIS (pH 5.5), 0.2 M (NH4)2SO4, 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: Feb 11, 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: 2.7→32 Å / Num. obs: 64080 / % possible obs: 97.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.59 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.119 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.7→2.77 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4449 / CC1/2: 0.844 / Rpim(I) all: 0.396 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ljj Resolution: 2.7→31.57 Å / SU ML: 0.3317 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0048 / 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: 20.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→31.57 Å
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Refine LS restraints |
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LS refinement shell |
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