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- PDB-6b1s: Hydrogen Bonding Complementary, not size complementarity is key i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6b1s | ||||||
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Title | Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Protein-DNA / AEGIS / unnatural base pair / host-guest system / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 | ![]() ![]() ![]() | ||||||
![]() | Singh, I. / Georgiadis, M.M. | ||||||
![]() | ![]() Title: "Skinny" and "Fat" DNA: Two New Double Helices. Authors: Hoshika, S. / Singh, I. / Switzer, C. / Molt Jr., R.W. / Leal, N.A. / Kim, M.J. / Kim, M.S. / Kim, H.J. / Georgiadis, M.M. / Benner, S.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 347.8 KB | Display | ![]() |
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PDB format | ![]() | 286.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.7 KB | Display | ![]() |
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Full document | ![]() | 468.9 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b1qC ![]() 6b1rC ![]() 4xo0S S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 29347.754 Da / Num. of mol.: 2 / Fragment: Catalytic fragment (UNP residues 683-937) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 4937.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.06 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 6 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 18, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→35.68 Å / Num. obs: 50699 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 27.72 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.046 / Rrim(I) all: 0.125 / Net I/σ(I): 14.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XO0 Resolution: 2→14.742 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→14.742 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -25.4365 Å / Origin y: 19.6976 Å / Origin z: 181.3079 Å
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Refinement TLS group | Selection details: all |