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- PDB-7xit: 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: 7xit | ||||||
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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 | ![]() | 45.6 KB | Display | ![]() |
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PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xisC ![]() 7xiuC ![]() 7xj4C ![]() 7xj5C ![]() 7xj7C ![]() 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-E6I / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.81 % / Mosaicity: 0.59 ° |
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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: 2.16→48.89 Å / Num. obs: 15758 / % possible obs: 99.7 % / Redundancy: 27.3 % / Biso Wilson estimate: 44.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.033 / Rrim(I) all: 0.169 / Net I/σ(I): 14.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QIN Resolution: 2.18→29.88 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 32.94 / 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: 140.55 Å2 / Biso mean: 50.1959 Å2 / Biso min: 23.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→29.88 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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