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- PDB-307d: Structure of a DNA analog of the primer for HIV-1 RT second stran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 307d | ||||||
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Title | Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis | ||||||
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![]() | DNA / B-DNA / DOUBLE HELIX | ||||||
Function / homology | DNA![]() | ||||||
Method | ![]() | ||||||
![]() | Han, G.W. / Kopka, M.L. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E. | ||||||
![]() | ![]() Title: Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis. Authors: Han, G.W. / Kopka, M.L. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45 KB | Display | ![]() |
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PDB format | ![]() | 31.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 393 KB | Display | ![]() |
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Full document | ![]() | 407.7 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.9 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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Unit cell |
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Components
#1: DNA chain | Mass: 3095.083 Da / Num. of mol.: 3 / Source method: obtained synthetically #2: DNA chain | Mass: 2991.961 Da / Num. of mol.: 3 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.63 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRROR MSC-YALE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100 Å / Num. obs: 9686 / % possible obs: 93.8 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.058 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5 / Rsym value: 0.24 / % possible all: 91 |
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 100 Å / % possible obs: 93.8 % / Rmerge(I) obs: 0.058 |
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Processing
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Refinement | Method to determine structure: MIR PHASE ANALYSIS Starting model: IDEAL B-DNA HELIX OF SEQUENCE CAAAGAAAAG Resolution: 1.85→8 Å / σ(F): 2 Details: THIS ENTRY PRESENTS THE COORDINATES OF THE CRYSTAL STRUCTURE OF CAAAGAAAAG AND ITS COMPLEMENTARY STRAND. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. HOWEVER, THE FIRST MOLECULE (HELIX #1 ...Details: THIS ENTRY PRESENTS THE COORDINATES OF THE CRYSTAL STRUCTURE OF CAAAGAAAAG AND ITS COMPLEMENTARY STRAND. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. HOWEVER, THE FIRST MOLECULE (HELIX #1 WITH STRANDS A AND B) IS ORDERED, AND THE SECOND MOLECULE IS DISORDERED WITH HELIX #2 (STRANDS C AND D) AND HELIX #3 (STRANDS E AND F). THIS IS EVIDENCED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD FROM ONE BROMINE AND ONE IODINE ISOMORPHOUS DERIVATIVE PLUS ANOMALOUS DATA. HELICES IN THE SECOND MOLECULE ARE DISORDERED END-FOR-END WITH HALF-WEIGHT HELICES #2 AND #3 BEING RELATED BY A TWOFOLD AXIS THROUGH THEIR CENTERS, NORMAL TO THE HELICAL AXIS. THE OCCUPANCY FOR THE HELIX #2 IS 0.52 AND FOR THE HELIX #3 IS 0.46.
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor Rwork: 0.233 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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