[English] 日本語
![](img/lk-miru.gif)
- PDB-5xx6: Hetero-micro-seeding: Crystal structure of BPTI-[5,55]C14GA38I va... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5xx6 | ||||||
---|---|---|---|---|---|---|---|
Title | Hetero-micro-seeding: Crystal structure of BPTI-[5,55]C14GA38I variant using micro-seeds from -C14GA38G variant | ||||||
![]() | Pancreatic trypsin inhibitor | ||||||
![]() | HYDROLASE / HYDROLASE INHIBITOR | ||||||
Function / homology | ![]() trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Islam, M.M. | ||||||
![]() | ![]() Title: A hetero-micro-seeding strategy for readily crystallizing closely related protein variants Authors: Islam, M.M. / Kuroda, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 44.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 29.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xx7C ![]() 5xx8C ![]() 2zvxS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 6409.323 Da / Num. of mol.: 2 / Mutation: A14G, A38I 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: 2.16 Å3/Da / Density % sol: 42.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20-30% PEG4000; 0.2M Lithium Sulfate; 0.1M Tris-HCl pH8.5 |
-Data collection
Diffraction | Mean temperature: 101 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: AGILENT EOS CCD / Detector: CCD / Date: Nov 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→53.22 Å / Num. obs: 26484 / % possible obs: 98 % / Redundancy: 3.6 % / Net I/σ(I): 4.34 |
Reflection shell | Resolution: 1.31→1.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 4.34 / Rsym value: 0.289 / % possible all: 98 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2ZVX Resolution: 1.31→53.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.878 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.062 / 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: 14.007 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.31→53.22 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|