[English] 日本語
![](img/lk-miru.gif)
- PDB-2qfp: Crystal structure of red kidney bean purple acid phosphatase in c... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2qfp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride | |||||||||
![]() | Purple acid phosphatase | |||||||||
![]() | ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Guddat, L.W. / Schenk, G.S. / Gahan, L.R. / Elliot, T.W. / Leung, E. | |||||||||
![]() | ![]() Title: Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle. Authors: Schenk, G. / Elliott, T.W. / Leung, E. / Carrington, L.E. / Mitic, N. / Gahan, L.R. / Guddat, L.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 364.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 299.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2qfrC ![]() 4kbpS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 20 molecules ABCD![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 49312.117 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O24319, UniProt: P80366*PLUS, ![]() #6: Sugar | ChemComp-NAG / ![]() |
---|
-Non-polymers , 6 types, 578 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/F.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/F.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE / ![]() #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / ![]() #5: Chemical | ChemComp-F / ![]() #7: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.78 % |
---|---|
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 10, 2005 / Details: mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→33 Å / Num. all: 142147 / Num. obs: 158646 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9434 / Rsym value: 0.34 / % possible all: 68.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 4KBP chain B and C Resolution: 2.2→33 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 36.365 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.624 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→33 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|