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Yorodumi- PDB-3dlk: Crystal Structure of an engineered form of the HIV-1 Reverse Tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dlk | ||||||
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Title | Crystal Structure of an engineered form of the HIV-1 Reverse Transcriptase, RT69A | ||||||
Components |
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Keywords | TRANSFERASE / AIDS / HIV / REVERSE TRANSCRIPTASE / RT / crystal engineering / RNA-binding / RNA-directed DNA polymerase / Viral nucleoprotein | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...HIV-1 retropepsin / : / 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-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 / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 BH10 Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å | ||||||
Authors | Ho, W.C. / Bauman, J.D. / Himmel, D.M. / Das, K. / Arnold, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2008 Title: Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design. Authors: Bauman, J.D. / Das, K. / Ho, W.C. / Baweja, M. / Himmel, D.M. / Clark, A.D. / Oren, D.A. / Boyer, P.L. / Hughes, S.H. / Shatkin, A.J. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dlk.cif.gz | 209.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dlk.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/3dlk ftp://data.pdbj.org/pub/pdb/validation_reports/dl/3dlk | HTTPS FTP |
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-Related structure data
Related structure data | 2zd1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 63946.211 Da / Num. of mol.: 1 / Fragment: p66 (UNP residues 599 to 1153) / Mutation: K172A, K173A, C258Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Strain: ISOLATE BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase |
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#2: Protein | Mass: 49531.871 Da / Num. of mol.: 1 / Fragment: p51 (UNP residues 605 to 1027) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, DNA-directed DNA polymerase, ribonuclease H |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 279.15 K / Method: vapor diffusion / Details: vapor diffusion, temperature 279.15K |
-Data collection
Diffraction | Mean temperature: 93.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.85→40.66 Å / Num. obs: 99442 |
-Processing
Software |
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Refinement | Starting model: PDB entry 2zd1 Resolution: 1.85→40.66 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 57.805 Å2 | ||||||||||||||||||||
Displacement parameters | Biso max: 150.19 Å2 / Biso mean: 50.143 Å2 / Biso min: 0.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→40.66 Å
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Refine LS restraints |
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Xplor file |
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