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Yorodumi- PDB-7xj5: Crystal structure of engineered HIV-1 Reverse Transcriptase RNase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xj5 | ||||||
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Title | Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with nitrofuran methoxy(methoxycarbonyl)phenyl ester | ||||||
Components | Reverse Transcriptase RNase H domain | ||||||
Keywords | VIRAL PROTEIN / ribonuclease | ||||||
Function / homology | Function and homology information 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Lu, H. / Komukai, Y. / Usami, K. / Guo, Y. / Qiao, X. / Nukaga, M. / Hoshino, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Chem.Inf.Model. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xj5.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xj5.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xj5_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7xj5_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7xj5_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 7xj5_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/7xj5 ftp://data.pdbj.org/pub/pdb/validation_reports/xj/7xj5 | HTTPS FTP |
-Related structure data
Related structure data | 7xisC 7xitC 7xiuC 7xj4C 7xj7C 3qinS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Human immunodeficiency virus 1 / Plasmid: pET50(b) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys References: UniProt: A0A059PIR4, UniProt: A0A7L9QW77, retroviral ribonuclease H | ||||||
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#2: Chemical | ChemComp-ECW / [ | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.95 % / Mosaicity: 0.26 ° |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2016 / 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: 1.75→49.33 Å / Num. obs: 30578 / % possible obs: 100 % / Redundancy: 27.4 % / Biso Wilson estimate: 23.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.023 / Rrim(I) all: 0.123 / Net I/σ(I): 31.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QIN Resolution: 1.75→34.4 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 32.48 / 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: 145.99 Å2 / Biso mean: 30.6611 Å2 / Biso min: 12.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→34.4 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %
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