+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pjg | ||||||
---|---|---|---|---|---|---|---|
Title | RNA/DNA Hybrid Decamer of CAAAGAAAAG/CTTTTCTTTG | ||||||
![]() |
| ||||||
![]() | DNA-RNA HYBRID / RNA/DNA hybrid / Polypurine Tract of HIV-1 / Moleuclar Replacement / sugar conformation / DNA-RNA COMPLEX | ||||||
Function / homology | DNA / RNA![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kopka, M.L. / Lavelle, L. / Han, G.W. / Ng, H.-L. / Dickerson, R.E. | ||||||
![]() | ![]() Title: An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H. Authors: Kopka, M.L. / Lavelle, L. / Han, G.W. / Ng, H.L. / Dickerson, R.E. #1: ![]() Title: Direct Methods Determination of an RNA/DNA Hybrid Decamer at 1.15A Resolution Authors: Han, G.W. #2: ![]() Title: Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation: Dimer Formation by Base-pair Swapping Authors: Han, G.W. / Kopka, M.L. / Langs, D. / Sawaya, M.R. / Dickerson, R.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 46.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 33.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 406 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pjoC C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 3255.076 Da / Num. of mol.: 1 / Fragment: Polypurine Tract of HIV-1 / Source method: obtained synthetically | ||
---|---|---|---|
#2: DNA chain | Mass: 2991.961 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: calcium acetate, cacodylate, beta-octylglucoside, spermidine hydrochloride, 2-methyl,2,4-pentanediol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 123 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 1999 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. obs: 17368 / % possible obs: 96.2 % / Observed criterion σ(I): 4.7 / Biso Wilson estimate: 8.17 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.15→1.18 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 11.09 / Num. unique all: 882 / % possible all: 93.9 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 96 % |
Reflection shell | *PLUS % possible obs: 93.9 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: NDB ID AH0001 Resolution: 1.15→8 Å / σ(F): 0
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.71 Å2 | |||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 1 / Occupancy sum non hydrogen: 1 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→8 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.15→1.18 Å /
| |||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.158 / Rfactor Rwork: 0.127 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|