[English] 日本語
![](img/lk-miru.gif)
- PDB-7xj4: Crystal structure of engineered HIV-1 Reverse Transcriptase RNase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7xj4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with nitrofuran methoxy(methoxycarbonyl)phenyl ester | ||||||
![]() | Reverse Transcriptase RNase H domain | ||||||
![]() | VIRAL PROTEIN / ribonuclease | ||||||
Function / homology | ![]() exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / nucleic acid binding / aspartic-type endopeptidase activity ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / nucleic acid binding / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lu, H. / Komukai, Y. / Usami, K. / Guo, Y. / Qiao, X. / Nukaga, M. / Hoshino, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. Authors: Lu, H. / Komukai, Y. / Usami, K. / Guo, Y. / Qiao, X. / Nukaga, M. / Hoshino, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 47.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 30.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7xisC ![]() 7xitC ![]() 7xiuC ![]() 7xj5C ![]() 7xj7C ![]() 3qinS 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: 16832.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A059PIR4, UniProt: A0A7L9QW77, retroviral ribonuclease H | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-E9B / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % / Mosaicity: 0.23 ° |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.1M MES, 26%(v/v) PEG 6000, 0.01M Zinc Sulfate, 0.001M MANGANESE CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2022 / Details: mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→48.74 Å / Num. obs: 27041 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 32.79 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.103 / Net I/σ(I): 13.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3QIN Resolution: 1.8→48.74 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 27.09 / 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: 81.71 Å2 / Biso mean: 40.4437 Å2 / Biso min: 20.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→48.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
|