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- PDB-1i6j: CRYSTAL STRUCTURE OF A PSEUDO-16-MER DNA WITH STACKED GUANINES AN... -
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Basic information
Entry | Database: PDB / ID: 1i6j | ||||||
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Title | CRYSTAL STRUCTURE OF A PSEUDO-16-MER DNA WITH STACKED GUANINES AND TWO G-A MISPAIRS COMPLEXED WITH THE N-TERMINAL FRAGMENT OF MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE | ||||||
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![]() | TRANSFERASE/DNA / Moloney Murine Leukemia Virus / Reverse Transcriptase / G-A Mispair / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cote, M.L. / Georgiadis, M.M. | ||||||
![]() | ![]() Title: Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase. Authors: Cote, M.L. / Georgiadis, M.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.8 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1d1uS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The second part of the DNA is generated by the 2-fold: -x-1, -y, z |
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Components
#1: DNA chain | Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ABI 392 DNA Synthesizer |
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#2: DNA chain | Mass: 3079.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ABI 392 DNA Synthesizer |
#3: Protein | Mass: 29065.480 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.74 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, NaCl, ADA, MgCl2, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 293 K | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 28, 2000 / Details: mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 25995 / Num. obs: 24781 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2163 / % possible all: 85.4 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 85.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1D1U Resolution: 2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati sigma a obs: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.225 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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