[English] 日本語
![](img/lk-miru.gif)
- PDB-6jpi: Crystal structure of PA4674 in complex with its operator DNA (28b... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6jpi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa | ||||||
![]() |
| ||||||
![]() | ANTITOXIN/DNA / Toxin-antitoxin system / transcription regulator / ANTITOXIN / ANTITOXIN-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Gao, Z. / Zhang, H. / Dong, Y. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa Authors: Liu, Y. / Gao, Z. / Zhang, H. / Dong, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 117.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 484.9 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3trbS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12232.791 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PA4674 Production host: ![]() ![]() References: UniProt: Q9HVC1 #2: DNA chain | | Mass: 8523.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: DNA chain | | Mass: 8683.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.1M MES, 35% 3-methyl-1,5-pentane diol, 0.2M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→50 Å / Num. obs: 11506 / % possible obs: 98.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 74 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.12 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.14→3.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 807 / CC1/2: 0.978 / Rrim(I) all: 0.754 / % possible all: 94.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3TRB Resolution: 3.143→45.35 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.57 / 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: 184.98 Å2 / Biso mean: 91.9144 Å2 / Biso min: 50.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.143→45.35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|