[English] 日本語
![](img/lk-miru.gif)
- PDB-5k54: Human muscle fructose-1,6-bisphosphatase E69Q mutant in active R-state -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5k54 | ||||||
---|---|---|---|---|---|---|---|
Title | Human muscle fructose-1,6-bisphosphatase E69Q mutant in active R-state | ||||||
![]() | Fructose-1,6-bisphosphatase isozyme 2 | ||||||
![]() | HYDROLASE / carbohydrate metabolism / glyconeogenesis / muscle izozyme / FBPase / R-state / Leucine lock / E69Q mutant | ||||||
Function / homology | ![]() sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / Gluconeogenesis / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc ...sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / Gluconeogenesis / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / anchoring junction / gluconeogenesis / Z disc / extracellular exosome / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Dzugaj, A. / Jaskolski, M. / Rakus, D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural studies of human muscle FBPase Authors: Barciszewski, J. / Szpotkowski, K. / Wisniewski, J. / Kolodziejczyk, R. / Jaskolski, M. / Rakus, D. / Dzugaj, A. #1: ![]() Title: Structure of E69Q mutant of human muscle fructose-1,6-bisphosphatase. Authors: Zarzycki, M. / Kolodziejczyk, R. / Maciaszczyk-Dziubinska, E. / Wysocki, R. / Jaskolski, M. / Dzugaj, A. #2: ![]() Title: Crystal structures of human muscle fructose-1,6-bisphosphatase: novel quaternary states, enhanced AMP affinity, and allosteric signal transmission pathway. Authors: Shi, R. / Chen, Z.Y. / Zhu, D.W. / Li, C. / Shan, Y. / Xu, G. / Lin, S.X. #3: ![]() Title: T-to-R switch of muscle fructose-1,6-bisphosphatase involves fundamental changes of secondary and quaternary structure. Authors: Barciszewski, J. / Wisniewski, J. / Kolodziejczyk, R. / Jaskolski, M. / Rakus, D. / Dzugaj, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 170.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5k55C ![]() 5k56C ![]() 5l0aC ![]() 5et5S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 36665.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: E69Q ENGINEERED MUTATION V85L IS A NATURAL VARIANT OF FBP2 Gaps in the sequence indicate residues that were not modeled because of poor electron density Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 10mM magnesium chloride, 2M sodium chloride, 10% PEG6000, 10mM Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 22, 2010 |
Radiation | Monochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.717→34.481 Å / Num. obs: 33575 / % possible obs: 99.5 % / Redundancy: 9.2 % / Biso Wilson estimate: 9.895 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.67 |
Reflection shell | Resolution: 1.717→1.82 Å / Redundancy: 7 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.25 / % possible all: 97.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5ET5 Resolution: 1.717→34.481 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / Phase error: 28.02 / Details: H ATOMS WERE ADDED AT RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.717→34.481 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|