[English] 日本語
![](img/lk-miru.gif)
- PDB-7esv: Structure and mutation analysis of the hexameric P4 from Pseudomo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7esv | ||||||
---|---|---|---|---|---|---|---|
Title | Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY | ||||||
![]() | Packaging NTPase | ||||||
![]() | HYDROLASE / Cystoviruses / phiYY P4(aa1-291) / NTPase / VIRAL PROTEIN | ||||||
Function / homology | Packaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / viral genome packaging / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / D(-)-TARTARIC ACID / Packaging NTPase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, C.Y. / Jin, T.C. | ||||||
![]() | ![]() Title: Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY. Authors: Zhang, C. / Li, Y. / Samad, A. / Zheng, P. / Ji, Z. / Chen, F. / Zhang, H. / Jin, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 156.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 122.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 867.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 879.8 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7esoC ![]() 7espC ![]() 7esqC ![]() 4blpS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30899.404 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: phiYY_sL4 / Production host: ![]() ![]() #2: Chemical | ChemComp-TAR / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 200 mM NH4 tartrate, 20% PEG2000 MME, phosphate pH 7.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→33.57 Å / Num. obs: 304717 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.993 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.18→2.24 Å / Num. unique obs: 22749 / CC1/2: 0.64 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4blp Resolution: 2.18→33.57 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.52 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.03 Å2 / Biso mean: 51.5898 Å2 / Biso min: 31.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→33.57 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|