+Open data
-Basic information
Entry | Database: PDB / ID: 1sli | ||||||
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Title | LEECH INTRAMOLECULAR TRANS-SIALIDASE COMPLEXED WITH DANA | ||||||
Components | INTRAMOLECULAR TRANS-SIALIDASE | ||||||
Keywords | HYDROLASE / INTRAMOLECULAR TRANS-SIALIDASE / NEURAMINIDASE | ||||||
Function / homology | Function and homology information anhydrosialidase / anhydrosialidase activity / exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Macrobdella decora (North American leech) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2 Å | ||||||
Authors | Luo, Y. / Li, S.C. / Chou, M.Y. / Li, Y.T. / Luo, M. | ||||||
Citation | Journal: Structure / Year: 1998 Title: The crystal structure of an intramolecular trans-sialidase with a NeuAc alpha2-->3Gal specificity. Authors: Luo, Y. / Li, S.C. / Chou, M.Y. / Li, Y.T. / Luo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sli.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sli.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sli_validation.pdf.gz | 811.9 KB | Display | wwPDB validaton report |
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Full document | 1sli_full_validation.pdf.gz | 819.7 KB | Display | |
Data in XML | 1sli_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 1sli_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/1sli ftp://data.pdbj.org/pub/pdb/validation_reports/sl/1sli | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 74565.688 Da / Num. of mol.: 1 / Fragment: DEVOID OF N-TERMINAL 28 RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrobdella decora (North American leech) Gene: T7 / Plasmid: E2-M10 / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q27701, exo-alpha-sialidase |
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#2: Sugar | ChemComp-DAN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.3 / Details: pH 6.3 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 24, 1997 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 53170 / % possible obs: 74 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.248 / % possible all: 56.3 |
Reflection | *PLUS Num. measured all: 72285 |
Reflection shell | *PLUS % possible obs: 56.3 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: NATIVE STRUCTURE Resolution: 2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 11.9 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 52955 / Rfactor obs: 0.182 / Rfactor Rfree: 0.228 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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