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Yorodumi- PDB-5xn1: HIV-1 reverse transcriptase Q151M:DNA:entecavir-triphosphate tern... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xn1 | |||||||||
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Title | HIV-1 reverse transcriptase Q151M:DNA:entecavir-triphosphate ternary complex | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / ENTECAVIR 5'-TRIPHOSPHATE / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / entecavir / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.446 Å | |||||||||
Authors | Yasutake, Y. / Tamura, N. / Hayashi, H. / Maeda, K. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir. Authors: Yasutake, Y. / Hattori, S.I. / Hayashi, H. / Matsuda, K. / Tamura, N. / Kohgo, S. / Maeda, K. / Mitsuya, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xn1.cif.gz | 886.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xn1.ent.gz | 726.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xn1_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5xn1_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5xn1_validation.xml.gz | 73.5 KB | Display | |
Data in CIF | 5xn1_validation.cif.gz | 99.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/5xn1 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/5xn1 | HTTPS FTP |
-Related structure data
Related structure data | 5xn0C 5xn2C 5d3gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 64033.387 Da / Num. of mol.: 2 / Fragment: p66 subunit (UNP RESIDUES 100-654) / Mutation: Q151M, C162S, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: D3XFN7, UniProt: P12497*PLUS #2: Protein | Mass: 51861.547 Da / Num. of mol.: 2 / Fragment: p51 subunit (UNP RESIDUES 100-527) / Mutation: C162S, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: D3XFN7, UniProt: P12497*PLUS |
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-DNA chain / Sugars , 2 types, 3 molecules EF
#3: DNA chain | Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose | |
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-Non-polymers , 4 types, 278 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20 mM bis-Tris-HCl pH 6.0, 60 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 1.5-3% PEG 6000, 2-4% sucrose, 4-8% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.446→50 Å / Num. obs: 106838 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rpim(I) all: 0.113 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.45→2.59 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D3G Resolution: 2.446→47.018 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.446→47.018 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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