[English] 日本語
![](img/lk-miru.gif)
- PDB-7a6g: Structural characterization of L-proline amide hydrolase from Pse... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7a6g | ||||||
---|---|---|---|---|---|---|---|
Title | Structural characterization of L-proline amide hydrolase from Pseudomonas syringae | ||||||
![]() | Putative Proline iminopeptidase | ||||||
![]() | HYDROLASE / ALPHA/BETA HYDROLASE FOLD | ||||||
Function / homology | Proline-specific peptidase / Peptidase S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / peptidase activity / Alpha/Beta hydrolase fold / PHOSPHATE ION / Putative Proline iminopeptidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martinez-Rodriguez, S. / Gavira, J.A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: A New L-Proline Amide Hydrolase with Potential Application within the Amidase Process Authors: Martinez-Rodriguez, S. / Contreras-Montoya, R. / Torres, J.M. / de Cienfuegos, L.A. / Gavira, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 144.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 112 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 429.8 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wmrS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 36750.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ALPHA/BETA HYDROLASE FOLD, HYDROLASE Source: (gene. exp.) ![]() Gene: ALO36_01328 / Plasmid: pET22b+ / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: HR1#28: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000 Temp details: 293 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2018 | ||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.95→42.731 Å / Num. obs: 20614 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.083 / Rrim(I) all: 0.191 / Net I/σ(I): 7.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3WMR Resolution: 1.95→42.731 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.03 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.51 Å2 / Biso mean: 21.671 Å2 / Biso min: 6.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→42.731 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|