[English] 日本語
![](img/lk-miru.gif)
- PDB-4hv7: Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylg... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4hv7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)glycine | ||||||
![]() | Ricin | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / RICIN / PROTEIN-LIGAND COMPLEX / PTERIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / TOXIN / HYDROLASE / RIBOSOME-INACTIVATING PROTEIN / N-GLYCOSIDASE | ||||||
Function / homology | ![]() rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / carbohydrate binding / toxin activity / killing of cells of another organism / negative regulation of translation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jasheway, K.R. / Monzingo, A.F. / Saito, R. / Pruet, J.M. / Manzano, L.A. / Wiget, P.A. / Anslyn, E.V. / Robertus, J.D. | ||||||
![]() | ![]() Title: Peptide-conjugated pterins as inhibitors of ricin toxin A. Authors: Saito, R. / Pruet, J.M. / Manzano, L.A. / Jasheway, K. / Monzingo, A.F. / Wiget, P.A. / Kamat, I. / Anslyn, E.V. / Robertus, J.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 74.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4huoC ![]() 4hupC ![]() 4hv3C ![]() 1rtcS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 29936.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: castor bean / Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-19J / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-MLA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2011 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.869→50 Å / Num. obs: 27776 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.89→1.92 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1RTC Resolution: 1.869→48.99 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8074 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.06 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.985 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.74 Å2 / Biso mean: 30.792 Å2 / Biso min: 14.05 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.869→48.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|