+Open data
-Basic information
Entry | Database: PDB / ID: 2fcx | |||||||||
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Title | HIV-1 DIS kissing-loop in complex with neamine | |||||||||
Components | HIV-1 DIS RNA | |||||||||
Keywords | RNA / HIV-1 / aminoglycoside / antibiotics | |||||||||
Function / homology | : / Chem-XXX / RNA / RNA (> 10) Function and homology information | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | |||||||||
Authors | Ennifar, E. / Paillart, J.C. / Marquet, R. / Dumas, P. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2006 Title: Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell. Authors: Ennifar, E. / Paillart, J.C. / Bodlenner, A. / Walter, P. / Weibel, J.-M. / Aubertin, A.-M. / Pale, P. / Dumas, P. / Marquet, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fcx.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fcx.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fcx_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2fcx_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2fcx_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 2fcx_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/2fcx ftp://data.pdbj.org/pub/pdb/validation_reports/fc/2fcx | 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: RNA chain | Mass: 7465.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in subtype F HIV-1 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Sugar | #5: 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: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7 Details: MPD, KCl, MgCl2, Na Cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 310K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→40 Å / Num. obs: 18852 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 54.5 Å2 / Rsym value: 0.074 / Net I/σ(I): 24.4 | |||||||||||||||
Reflection shell | Highest resolution: 2 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.273 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→36.42 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 791329.06 / Data cutoff high rms absF: 791329.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.9384 Å2 / ksol: 0.39033 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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