[English] 日本語
![](img/lk-miru.gif)
- PDB-2a9j: Human bisphosphoglycerate mutase complexed with 3-phosphoglycerat... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2a9j | ||||||
---|---|---|---|---|---|---|---|
Title | Human bisphosphoglycerate mutase complexed with 3-phosphoglycerate (17 days) | ||||||
![]() | Bisphosphoglycerate mutase | ||||||
![]() | ISOMERASE / bisphosphoglycerate mutase / 3-phosphoglycerate | ||||||
Function / homology | ![]() carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / defense response to protozoan ...carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / defense response to protozoan / oxygen transport / erythrocyte development / glycolytic process / carbohydrate metabolic process / hydrolase activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wang, Y. / Gong, W. | ||||||
![]() | ![]() Title: Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase Authors: Wang, Y. / Liu, L. / Wei, Z. / Cheng, Z. / Lin, Y. / Gong, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 95.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457 KB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f90C ![]() 2h4xC ![]() 2h4zC ![]() 2hhjC ![]() 1zst ![]() 1zsu ![]() 2a17 ![]() 2a1p ![]() 2a1q C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The dimer is the biological units. |
-
Components
#1: Protein | Mass: 31118.375 Da / Num. of mol.: 2 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: 2.18 Å3/Da / Density % sol: 43.11 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 37400 / Num. obs: 37400 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 45.3 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 17.7 / Num. unique all: 2478 / % possible all: 96.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5197 Å2 / ksol: 0.31658 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.1 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|