+Open data
-Basic information
Entry | Database: PDB / ID: 8ul7 | ||||||
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Title | The structure of NanH in complex with Neu5Ac | ||||||
Components | Sialidase | ||||||
Keywords | HYDROLASE / Sialidase | ||||||
Function / homology | Function and homology information ganglioside catabolic process / oligosaccharide catabolic process / : / : / : / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Clostridium perfringens ATCC 13124 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Medley, B.J. / Boraston, A.B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: A "terminal" case of glycan catabolism: structural and enzymatic characterization of the sialidases of Clostridium perfringens. Authors: Medley, B.J. / Low, K.E. / Irungu, J.D.W. / Kipchumba, L. / Daneshgar, P. / Liu, L. / Garber, J.M. / Klassen, L. / Inglis, G.D. / Boons, G.J. / 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 | 8ul7.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ul7.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 8ul7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ul7_validation.pdf.gz | 820.4 KB | Display | wwPDB validaton report |
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Full document | 8ul7_full_validation.pdf.gz | 820.3 KB | Display | |
Data in XML | 8ul7_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 8ul7_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/8ul7 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/8ul7 | HTTPS FTP |
-Related structure data
Related structure data | 8u2aC 8u5oC 8ub5C 8uleC 8um0C 8uvvC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43066.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria) Gene: nanH / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B1V1R3 | ||||||
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#2: Chemical | ChemComp-EDO / #3: Sugar | ChemComp-SIA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES:NaOH pH 7.5, 20% PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.534 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.534 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→23 Å / Num. obs: 36096 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.997 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.85→1.9 Å / Num. unique obs: 1823 / CC1/2: 0.782 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→22.91 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→22.91 Å
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Refine LS restraints |
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LS refinement shell |
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