[English] 日本語
![](img/lk-miru.gif)
- PDB-6vcl: Crystal structure of E.coli RppH-DapF in complex with pppGpp, Mg2... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vcl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E.coli RppH-DapF in complex with pppGpp, Mg2+ and F- | ||||||
![]() |
| ||||||
![]() | RNA BINDING PROTEIN/ISOMERASE / RNA degradation / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH. Authors: Gao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 115.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6vckC ![]() 6vcmC ![]() 6vcnC ![]() 6vcoC ![]() 6vcpC ![]() 6vcqC ![]() 6vcrC ![]() 6d1vS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 30154.422 Da / Num. of mol.: 1 / Mutation: R36A, Y268A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: dapF, b3809, JW5592 / Production host: ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 18965.773 Da / Num. of mol.: 1 / Mutation: Q159A, E160A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: ![]() ![]() ![]() References: UniProt: P0A776, ![]() |
-Non-polymers , 6 types, 290 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/F.gif)
![](data/chem/img/0O2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/F.gif)
![](data/chem/img/0O2.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-MG / #5: Chemical | ![]() #6: Chemical | ChemComp-F / | ![]() #7: Chemical | ChemComp-0O2 / | #8: Water | ChemComp-HOH / | ![]() |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.28 % |
---|---|
Crystal grow![]() | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 9.2 / Details: 30% (v/v) PEG400, 0.1 M CHES, pH 9.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→30 Å / Num. obs: 48690 / % possible obs: 98.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.98 Å2 / CC1/2: 0.996 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.05→2.09 Å / Num. unique obs: 2296 / CC1/2: 0.607 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 6D1V Resolution: 2.06→30 Å / SU ML: 0.2454 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1725
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|