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Yorodumi- PDB-3c3z: Crystal structure of HIV-1 subtype F DIS extended duplex RNA boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c3z | ||||||
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Title | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin | ||||||
Components | HIV-1 subtype F genomic RNA | ||||||
Keywords | RNA / HIV-1 / antibiotic | ||||||
Function / homology | RIBOSTAMYCIN / DNA/RNA hybrid / DNA/RNA hybrid (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Freisz, S. / Lang, K. / Micura, R. / Dumas, P. / Ennifar, E. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2008 Title: Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site. Authors: Freisz, S. / Lang, K. / Micura, R. / Dumas, P. / Ennifar, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c3z.cif.gz | 41.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c3z.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 3c3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c3z_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3c3z_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3c3z_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 3c3z_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/3c3z ftp://data.pdbj.org/pub/pdb/validation_reports/c3/3c3z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA/RNA hybrid | Mass: 7463.459 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: 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: 2.51 Å3/Da / Density % sol: 51.02 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 300mM KCl, 2mM MgCl2, 50mM Na Cacodylate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9788, 0.9793, 0.9732 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2006 | ||||||||||||
Radiation | Monochromator: crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→30 Å / Num. obs: 46246 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 27.9 | ||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 4602 / Rsym value: 0.243 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→18.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 868917.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1428 Å2 / ksol: 0.383433 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→18.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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