[English] 日本語
![](img/lk-miru.gif)
- PDB-2bf6: Atomic Resolution Structure of the bacterial sialidase NanI from ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2bf6 | ||||||
---|---|---|---|---|---|---|---|
Title | Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac). | ||||||
![]() | EXO-ALPHA-SIALIDASE | ||||||
![]() | HYDROLASE / SIALIDASE / CLOSTRIDIUM PERFRINGENS / SIALIC ACID | ||||||
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. / 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 |
| ||||||
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. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 209 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 162 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 857.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 862.7 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vk5C ![]() 2vk6C ![]() 2vk7C ![]() 1sllS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 50091.492 Da / Num. of mol.: 1 / Fragment: RESIDUES 243-691 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Sugar | ChemComp-SIA / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 49 % |
---|---|
Crystal grow | pH: 7 / Details: 20 % PEG 3350, 0.2M POTASSIUM NITRATE, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 20, 2004 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / 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→57 Å / Num. obs: 290992 / % possible obs: 91 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 0.97→1.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5 / % possible all: 87 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SLL Resolution: 0.97→57 Å / Num. parameters: 36804 / Num. restraintsaints: 44962 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.0
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 3285.2 / Occupancy sum non hydrogen: 4037.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→57 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|