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Open data
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Basic information
Entry | Database: PDB / ID: 1duq | ||||||
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Title | CRYSTAL STRUCTURE OF THE REV BINDING ELEMENT OF HIV-1 | ||||||
![]() | (THE REV BINDING ELEMENT) x 2 | ||||||
![]() | RNA / RRE / HIV-1 / REV BINDING DOMAIN | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hung, L.-W. / Holbrook, E.L. / Holbrook, S.R. | ||||||
![]() | ![]() Title: The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability. Authors: Hung, L.W. / Holbrook, E.L. / Holbrook, S.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.8 KB | Display | ![]() |
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PDB format | ![]() | 51.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372 KB | Display | ![]() |
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Full document | ![]() | 376 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 3922.400 Da / Num. of mol.: 4 / Fragment: SHORT CHAIN / Source method: obtained synthetically / Details: SEQUENCE FROM HIV-1. SYNTHESIZED BY OLIGOS, ETC. #2: RNA chain | Mass: 4461.723 Da / Num. of mol.: 4 / Fragment: LONG CHAIN / Source method: obtained synthetically #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.19 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M SODIUM CACODYLATE, PH 6.5, 0.2 M NACL, 35% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 16703 / Num. obs: 15998 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.38 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.248 / % possible all: 83.2 |
Reflection shell | *PLUS % possible obs: 83 % |
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Processing
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Refinement | Resolution: 2.1→19.77 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 659115.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.11 Å2 / ksol: 0.399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.385 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.301 |