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Yorodumi- PDB-7dbn: HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V/F160M:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dbn | ||||||
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Title | HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V/F160M:DNA:dCTP ternary complex | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Entecavir 5'-triphosphate / HIV-1 / HBV / reverse transcriptase / drug resistance / TRANSFERASE-DNA complex / REPLICATION | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Human immunodeficiency virus type 1 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Yasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Virol. / Year: 2021 Title: Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations. Authors: Nakajima, S. / Watashi, K. / Kato, T. / Muramatsu, M. / Wakita, T. / Tamura, N. / Hattori, S.I. / Maeda, K. / Mitsuya, H. / Yasutake, Y. / Toyoda, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dbn.cif.gz | 890.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dbn.ent.gz | 733.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/7dbn ftp://data.pdbj.org/pub/pdb/validation_reports/db/7dbn | HTTPS FTP |
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-Related structure data
Related structure data | 7dbmC 6kdjS 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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1 |
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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: 63985.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: D3XFN5, RNA-directed DNA polymerase, retroviral ribonuclease H #2: Protein | Mass: 51861.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497 |
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-DNA chain , 1 types, 2 molecules EF
#3: DNA chain | Mass: 11764.525 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 190 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.96 Å3/Da / Density % sol: 58.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL |
-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: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→50 Å / Num. obs: 83121 / % possible obs: 100 % / Redundancy: 5.4 % / Rrim(I) all: 0.089 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.67→2.72 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4525 / Rrim(I) all: 0.982 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KDJ Resolution: 2.67→48.895 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.27 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→48.895 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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