[English] 日本語
![](img/lk-miru.gif)
- PDB-1yr2: Structural and Mechanistic Analysis of Two Prolyl Endopeptidases:... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1yr2 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Inter-Domain Dynamics in Catalysis and Specificity | ||||||
![]() | prolyl oligopeptidase | ||||||
![]() | HYDROLASE / prolyl endopeptidase / mechanistic study / celiac sprue | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shan, L. / Mathews, I.I. / Khosla, C. | ||||||
![]() | ![]() Title: Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Interdomain Dynamics in Catalysis and Specificity Authors: Shan, L. / Mathews, I.I. / Khosla, C. #1: Journal: Biochem.J. / Year: 2004 Title: Comparative biochemical analysis of three bacterial prolyl endopeptidases: implications for celiac sprue Authors: Shan, L. / Marti, T. / Sollid, L.M. / Gray, G.M. / Khosla, C. #2: Journal: Science / Year: 2002 Title: Structural basis for gluten intolerance in Celiac Sprue Authors: Shan, L. / Molberg, O. / Parroit, I. / Hausch, F. / Filiz, F. / Gray, G.M. / Sollid, L.M. / Khosla, C. #3: ![]() Title: The prolyl oligopeptidase family Authors: Polgar, L. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE The conflict may be due to a different lab strain. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 159.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 123.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 383.4 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bklC ![]() 1h2wS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 80657.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: PEG 8000, Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 11, 2003 / Details: monochromator |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 68648 / Num. obs: 68648 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.071 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 6381 / Rsym value: 0.502 / % possible all: 92.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H2W Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.545 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.553 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|