[English] 日本語
![](img/lk-miru.gif)
- PDB-5bwy: Structure of proplasmepsin II from Plasmodium falciparum, Space G... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5bwy | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of proplasmepsin II from Plasmodium falciparum, Space Group P43212 | ||||||
![]() | Plasmepsin-2 | ||||||
![]() | HYDROLASE / malaria | ||||||
Function / homology | ![]() cytostome / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Recacha, R. / Akopjana, I. / Tars, K. / Jaudzems, K. | ||||||
![]() | ![]() Title: Crystal structure of Plasmodium falciparum proplasmepsin IV: the plasticity of proplasmepsins. Authors: Recacha, R. / Jaudzems, K. / Akopjana, I. / Jirgensons, A. / Tars, K. #1: ![]() Title: Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from plasmodium falciparum. Authors: Bernstein, N.K. / Cherney, M.M. / Loetscher, H. / Ridley, R.G. / James, M.N. #2: ![]() Title: Structural insights into the activation of P. vivax plasmepsin. Authors: Bernstein, N.K. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 167.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 133.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 427.7 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jodC ![]() 1pfzS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42374.969 Da / Num. of mol.: 1 / Fragment: UNP residues 78-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PFAG_05140 / Plasmid: pET3A / Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M Sodium Citrate, 0.1 M Sodium Acetate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: May 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→44.7 Å / Num. all: 14252 / Num. obs: 14252 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.64→2.76 Å / Redundancy: 5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1PFZ Resolution: 2.644→44.69 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.46 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.644→44.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|