[English] 日本語
![](img/lk-miru.gif)
- PDB-7wa2: Crystal structure of Bovine Pancreatic Trypsin in complex with 4-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7wa2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Bovine Pancreatic Trypsin in complex with 4-Methoxybenzamidine at Room Temperature | ||||||
![]() | Cationic trypsin | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sakai, N. / Okumura, H. / Yamamoto, M. / Kumasaka, T. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: In situ crystal data-collection and ligand-screening system at SPring-8. Authors: Okumura, H. / Sakai, N. / Murakami, H. / Mizuno, N. / Nakamura, Y. / Ueno, G. / Masunaga, T. / Kawamura, T. / Baba, S. / Hasegawa, K. / Yamamoto, M. / Kumasaka, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 658.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 658.6 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wa0C ![]() 7wb6C ![]() 7wb7C ![]() 7wb8C ![]() 7wb9C ![]() 7wbaC ![]() 1s0rS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: Chemical | ChemComp-RKX / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100mM Tris-HCl, 30% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. obs: 30897 / % possible obs: 91.4 % / Redundancy: 3.47 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 0.987 / Rrim(I) all: 0.177 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.52→1.61 Å / Redundancy: 3.68 % / Mean I/σ(I) obs: 2.48 / Num. unique obs: 4690 / CC1/2: 0.535 / Rrim(I) all: 1.212 / % possible all: 88.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1S0R Resolution: 1.52→39.88 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.139 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.069 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.975 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.52→39.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|