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- PDB-7xj7: Crystal structure of engineered HIV-1 Reverse Transcriptase RNase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xj7 | ||||||
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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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.2 KB | Display | ![]() |
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PDB format | ![]() | 30.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xisC ![]() 7xitC ![]() 7xiuC ![]() 7xj4C ![]() 7xj5C ![]() 3qinS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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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 | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EGI / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.95 % / Mosaicity: 0.25 ° |
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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 | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 20, 2017 / 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: 1.73→48.96 Å / Num. obs: 16864 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 28.65 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 28.2 / Num. measured all: 227865 / Scaling rejects: 96 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 3QIN Resolution: 1.8→29.77 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.86 Å2 / Biso mean: 34.7001 Å2 / Biso min: 15.81 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→29.77 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %
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