[English] 日本語
![](img/lk-miru.gif)
- PDB-2b5u: Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2b5u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein | ||||||
![]() |
| ||||||
![]() | RIBOSOME INHIBITOR / HYDROLASE / High resolution crystal structure / Colicin E3 / Immunity Protein / Ribosome inactivation | ||||||
Function / homology | ![]() negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / tRNA binding ...negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / tRNA binding / rRNA binding / lyase activity / defense response to bacterium / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nallini Vijayarangan, A. / Nithianantham, S. / Nan, W. / Jakes, K. / Shoham, M. | ||||||
![]() | ![]() Title: Crystal Structure Of Colicin E3 In Complex With Its Immunity Protein Authors: Nallini Vijayarangan, A. / Nithianantham, S. / Nan, W. / Jakes, K. / Shoham, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 225.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 179.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 496.5 KB | Display | |
Data in XML | ![]() | 43.1 KB | Display | |
Data in CIF | ![]() | 59.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jchS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 58047.023 Da / Num. of mol.: 2 / Mutation: V206C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() Strain (production host): W3110 References: UniProt: P00646, Hydrolases; Acting on ester bonds #2: Protein | Mass: 9779.565 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() Strain (production host): W3110 / References: UniProt: P02984 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 66 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.6 Details: Sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Aug 3, 2005 / Details: Mirrors |
Radiation | Monochromator: Si-111, Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 88792 / Num. obs: 88240 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Χ2: 1 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible obs: 97.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.465 / Num. measured obs: 8682 / Χ2: 1.37 / % possible all: 97 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JCH Resolution: 2.3→44.4 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 39.605 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.725 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.4 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|