[English] 日本語
![](img/lk-miru.gif)
- PDB-7lc7: Crystal structure of epoxyqueuosine reductase QueH in complex wit... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7lc7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of epoxyqueuosine reductase QueH in complex with GMP from Thermotoga maritima | ||||||
![]() | Epoxyqueuosine reductase QueH | ||||||
![]() | OXIDOREDUCTASE / Epoxyqueuosine Reductase / QueH / Iron-Sulfur Cluster / GMP / Queuosine / tRNA | ||||||
Function / homology | ![]() epoxyqueuosine reductase / epoxyqueuosine reductase activity / queuosine biosynthetic process / tRNA processing / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, Q. / Bruner, S.D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The epoxyqueuosine reductase QueH in the biosynthesis of tRNA queuosine is a unique metalloenzyme Authors: Li, Q. / Bruner, S.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 64.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 37.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lc5S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22548.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: queH, TM_0731 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 90 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / |
---|---|
#3: Chemical | ChemComp-5GP / |
#4: Chemical | ChemComp-FE / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Bis-Tris, pH 5.5, 200 mM lithium sulfate monohydrate, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2018 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.576→47.53 Å / Num. obs: 27990 / % possible obs: 96.78 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.24 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07859 / Rpim(I) all: 0.03314 / Rrim(I) all: 0.08552 / Net I/σ(I): 13.25 |
Reflection shell | Resolution: 1.576→1.633 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.6747 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 2694 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.2866 / Rrim(I) all: 0.7346 / % possible all: 94.29 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 7LC5 Resolution: 1.58→47.53 Å / SU ML: 0.1881 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5557 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→47.53 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|