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Yorodumi- PDB-3ith: Crystal structure of the HIV-1 reverse transcriptase bound to a 6... -
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-Basic information
Entry | Database: PDB / ID: 3ith | ||||||
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Title | Crystal structure of the HIV-1 reverse transcriptase bound to a 6-vinylpyrimidine inhibitor | ||||||
Components |
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Keywords | TRANSFERASE / HYDROLASE / HIV-1 / inhibitor / RT | ||||||
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 / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Freisz, S. / Bec, G. / Wolff, P. / Dumas, P. / Radi, M. / Botta, M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010 Title: Crystal Structure of HIV-1 Reverse Transcriptase Bound to a Non-Nucleoside Inhibitor with a Novel Mechanism of Action Authors: Freisz, S. / Bec, G. / Radi, M. / Wolff, P. / Crespan, E. / Angeli, L. / Dumas, P. / Maga, G. / Botta, M. / Ennifar, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ith.cif.gz | 395.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ith.ent.gz | 323.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ith.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/3ith ftp://data.pdbj.org/pub/pdb/validation_reports/it/3ith | HTTPS FTP |
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-Related structure data
Related structure data | 3isnC 1dloS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64516.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus / Strain: type 1 BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H #2: Protein | Mass: 49927.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus / Strain: type 1 BH10 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366 #3: Chemical | Sequence details | E465Q IS MUTAGENESI | |
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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: 3.14 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350, 100mM Hepes, 200mM ammonium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→44 Å / Num. all: 136888 / Num. obs: 116796 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 79.78 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.052 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7811 / Rsym value: 0.592 / % possible all: 57.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DLO Resolution: 2.8→43.895 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.746 / SU ML: 0.32 / σ(F): 1.99 / σ(I): 0 / Phase error: 31.87 / Stereochemistry target values: ML / Details: THE FILE CONTAINS FRIEDEL PAIRS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.931 Å2 / ksol: 0.305 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 182.91 Å2 / Biso mean: 91.144 Å2 / Biso min: 40.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→43.895 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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