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- PDB-2vk5: THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vk5 | ||||||
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Title | THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES | ||||||
![]() | EXO-ALPHA-SIALIDASE | ||||||
![]() | HYDROLASE / SIALIDASE / GLYCOSIDASE / SIALIC ACID / CLOSTRIDIUM PERFRINGENS | ||||||
Function / homology | ![]() ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newstead, S.L. / Potter, J.A. / Wilson, J.C. / Xu, G. / Chien, C.H. / Watts, A.G. / Withers, S.G. / Taylor, G.L. | ||||||
![]() | ![]() Title: The Structure of Clostridium Perfringens Nani Sialidase and its Catalytic Intermediates. Authors: Newstead, S.L. / Potter, J.A. / Wilson, J.C. / Xu, G. / Chien, C.H. / Watts, A.G. / Withers, S.G. / Taylor, G.L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.9 KB | Display | ![]() |
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PDB format | ![]() | 183.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440 KB | Display | ![]() |
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Full document | ![]() | 447.7 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 50.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bf6C ![]() 2vk6C ![]() 2vk7C ![]() 1sllS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50405.852 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 243-694 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→20 Å / Num. obs: 281317 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 0.97→1.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.6 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SLL Resolution: 0.97→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 0.97→20 Å
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Refine LS restraints |
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