[English] 日本語
![](img/lk-miru.gif)
- PDB-3n2w: Crystal structure of the N-terminal beta-aminopeptidase BapA from... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3n2w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal beta-aminopeptidase BapA from Sphingosinicella xenopeptidilytica | ||||||
![]() | Beta-peptidyl aminopeptidase | ||||||
![]() | HYDROLASE / Ntn hydrolase / alpha-beta-beta-alpha sandwich / beta-aminopeptidase / beta-peptide | ||||||
Function / homology | ![]() beta-peptidyl aminopeptidase / aminopeptidase activity / periplasmic space / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Merz, T. / Heck, T. / Geueke, B. / Kohler, H.-P. / Gruetter, M.G. | ||||||
![]() | ![]() Title: Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family. Authors: Merz, T. / Heck, T. / Geueke, B. / Mittl, P.R. / Briand, C. / Seebach, D. / Kohler, H.P. / Grutter, M.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 552 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 458.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 494.8 KB | Display | |
Data in XML | ![]() | 69.2 KB | Display | |
Data in CIF | ![]() | 105.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n33C ![]() 3n5iC ![]() 1b65S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38634.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: bapA / Plasmid: pYBapA / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.29 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.5M Ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→48.809 Å / Num. all: 282888 / Num. obs: 278550 / % possible obs: 98.5 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.075 / Rsym value: 0.042 / Net I/σ(I): 16.99 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.67 / Rsym value: 0.433 / % possible all: 92.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B65 Resolution: 1.45→48.809 Å / SU ML: 0.15 / Isotropic thermal model: isotropic / σ(F): 1.99 / Phase error: 13.42 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.577 Å2 / ksol: 0.427 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→48.809 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|