[English] 日本語
![](img/lk-miru.gif)
- PDB-5x8z: Unique Choloylglycine Hydrolase(CGH) member from Shewanella loihi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5x8z | ||||||
---|---|---|---|---|---|---|---|
Title | Unique Choloylglycine Hydrolase(CGH) member from Shewanella loihica PV-4 | ||||||
![]() | Penicillin V acylase-like protein | ||||||
![]() | HYDROLASE / Choloylglycine Hydrolase / BSH / PVA like / AHL activity | ||||||
Function / homology | Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / hydrolase activity / Penicillin V acylase-like protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramasamy, S. / Philem, P.D. / Yadav, Y. | ||||||
![]() | ![]() Title: Unique Choloylglycine Hydrolase(CGH) member from Shewanella loihica PV-4 Authors: Philem, P.D. / Yadav, Y. / Prabune, A.A. / Ramasamy, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 141.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 110.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x9iC ![]() 3hbcS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37944.449 Da / Num. of mol.: 2 / Fragment: UNP residues 27-359 Source method: isolated from a genetically manipulated source Details: Marine bacteria / Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 48.58 % / Description: Elongated needles |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 3350, sodium sulphate, 2-Methyl-2, 4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 15, 2015 |
Radiation | Monochromator: Double crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→89.43 Å / Num. obs: 109332 / % possible obs: 97.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3HBC Resolution: 1.5→89.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.275 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.076 / 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: 14.372 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→89.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|