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Open data
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Basic information
Entry | Database: PDB / ID: 8gn6 | ||||||
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Title | Crystallization of Sialidase from Porphyromonas gingivalis | ||||||
![]() | (Sialidase) x 2 | ||||||
![]() | CARBOHYDRATE / sialidase | ||||||
Function / homology | BNR repeat-like domain / exo-alpha-sialidase activity / Sialidase family / Sialidase / Sialidase superfamily / Unknown ligand / Sialidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, W.B. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural and enzymatic characterization of the sialidase SiaPG from Porphyromonas gingivalis. Authors: Dong, W.B. / Jiang, Y.L. / Zhu, Z.L. / Zhu, J. / Li, Y. / Xia, R. / Zhou, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.6 KB | Display | ![]() |
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PDB format | ![]() | 252.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
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Full document | ![]() | 462.1 KB | Display | |
Data in XML | ![]() | 59.1 KB | Display | |
Data in CIF | ![]() | 86.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6myvS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 58452.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A1R4DV85 #2: Protein | | Mass: 58167.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A1R4DV85 #3: Chemical | Mass: 103.120 Da / Num. of mol.: 3 / Source method: obtained synthetically #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.92 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 1.4M Ammonium tartrate dibasic,0.1M Tris PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→56.86 Å / Num. obs: 101168 / % possible obs: 95.8 % / Redundancy: 15.3 % / CC1/2: 0.999 / Net I/σ(I): 48.4 |
Reflection shell | Resolution: 2.1→2.2381 Å / Num. unique obs: 101168 / CC1/2: 1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6MYV Resolution: 2.1→56.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.969 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.539 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→56.86 Å
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Refine LS restraints |
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