[English] 日本語
![](img/lk-miru.gif)
- PDB-5jex: Crystal structure of type 2 PDF from Streptococcus agalactiae, cr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5jex | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of type 2 PDF from Streptococcus agalactiae, crystallized in imidazole buffer | ||||||
![]() | Peptide deformylase | ||||||
![]() | HYDROLASE / PDF / type 2 / NME / N-terminal methionine excision / Streptococcus agalactiae / inhibitor | ||||||
Function / homology | ![]() peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fieulaine, S. / Giglione, C. / Meinnel, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: A unique peptide deformylase platform to rationally design and challenge novel active compounds. Authors: Fieulaine, S. / Alves de Sousa, R. / Maigre, L. / Hamiche, K. / Alimi, M. / Bolla, J.M. / Taleb, A. / Denis, A. / Pages, J.M. / Artaud, I. / Meinnel, T. / Giglione, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.9 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jeyC ![]() 5jezC ![]() 5jf0C ![]() 5jf1C ![]() 5jf2C ![]() 5jf3C ![]() 5jf4C ![]() 5jf5C ![]() 5jf6C ![]() 5jf7C ![]() 5jf8C ![]() 2aieS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22894.297 Da / Num. of mol.: 1 / Mutation: S2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-IMD / | ||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.12 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 7% PEG-8000 , 100mM Imidazole pH7.5, 300mM Zn Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9755 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 16886 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.09 / Net I/σ(I): 17.04 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 6.63 / Rsym value: 0.295 / % possible all: 99.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2AIE Resolution: 2→44.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.254 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.111 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→44.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|