[English] 日本語
![](img/lk-miru.gif)
- PDB-5img: C9A mutant of C69-family cysteine dipeptidase from Lactobacillus ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5img | ||||||
---|---|---|---|---|---|---|---|
Title | C9A mutant of C69-family cysteine dipeptidase from Lactobacillus farciminis | ||||||
![]() | Dipeptidase | ||||||
![]() | HYDROLASE / C69 family / cysteine dipeptidase / Ntn hydrolase / Lactobacillus farciminis / Gly-Pro | ||||||
Function / homology | : / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kono, R. / Watanabe, K. | ||||||
![]() | ![]() Title: A C69-family cysteine dipeptidase from Lactobacillus farciminis; substrate recognition mechanism and autoproteolytic mechanism in enzyme maturation Authors: Kono, R. / Watanabe, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 848.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 505.1 KB | Display | |
Data in XML | ![]() | 213.1 KB | Display | |
Data in CIF | ![]() | 333 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5iauSC ![]() 5imhC ![]() 5inrC ![]() 5inxC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 52872.277 Da / Num. of mol.: 10 / Mutation: C9A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: KCTC 3681 = DSM 20184 / Gene: FC68_GL001211 / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CO / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 0.6 M 1,6-hexanediol, 19 mM CoCl2, 100 mM acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.844→40.526 Å / Num. obs: 449987 / % possible obs: 96.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 22.65 |
Reflection shell | Resolution: 1.844→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 5.11 / % possible all: 92.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5IAU Resolution: 1.844→40.526 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.58 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.844→40.526 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|