[English] 日本語
![](img/lk-miru.gif)
- PDB-4cyy: The structure of vanin-1: defining the link between metabolic dis... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4cyy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation | |||||||||
![]() | PANTETHEINASE | |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Boersma, Y.L. / Newman, J. / Adams, T.E. / Sparrow, L. / Cowieson, N. / Lucent, D. / Krippner, G. / Bozaoglu, K. / Peat, T.S. | |||||||||
![]() | ![]() Title: The Structure of Vanin-1: A Key Enzyme Linking Metabolic Disease and Inflammation Authors: Boersma, Y.L. / Newman, J. / Adams, T.E. / Cowieson, N. / Krippner, G. / Bozaoglu, K. / Peat, T.S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 109.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4cyfSC ![]() 4cygC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 56325.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FLAG-TAG AT THE N-TERMINUS AND PRO-PEPTIDE AT THE C-TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE FORM OF THE PROTEIN. Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||||
#3: Sugar | ChemComp-NAG / ![]() #4: Water | ChemComp-HOH / | ![]() Sequence details | FLAG TAG AT N-TERMINUS AND THE PRO-PEPTIDE AT THE C- TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE ...FLAG TAG AT N-TERMINUS AND THE PRO-PEPTIDE AT THE C- TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE FORM OF THE PROTEIN. IN ADDITION THE DEPOSITED STRUCTURE HAS THE NATURALLY OCCURRING THR26ILE SNP IN THE SEQUENCE. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.6 % / Description: NONE |
---|---|
Crystal grow![]() | Method: vapor diffusion, sitting drop / pH: 6 Details: THE PROTEIN WAS AT 15 MG/ML. THE RESERVOIR CONDITIONS WERE 25% (W/V) PEG 1500 PLUS 10% (V/V) SUCCINATE-PHOSPHATE-GLYCINE BUFFER AT PH 6.0. THE PLATES WERE SET UP AT 8 C AND THE DROPS WERE ...Details: THE PROTEIN WAS AT 15 MG/ML. THE RESERVOIR CONDITIONS WERE 25% (W/V) PEG 1500 PLUS 10% (V/V) SUCCINATE-PHOSPHATE-GLYCINE BUFFER AT PH 6.0. THE PLATES WERE SET UP AT 8 C AND THE DROPS WERE 150 NL PLUS 150 NL IN SITTING DROP PLATES. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.89→47.6 Å / Num. obs: 18526 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 16.3 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.89→3.04 Å / Redundancy: 16.1 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.7 / % possible all: 97.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4CYF Resolution: 2.89→88.25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.219 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.6 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 61.539 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→88.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|