Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
1n7b
Class
DNA, RNA
Method
X-ray (1.4 Å)
Summary
Rip-radiation-damage induced phasing
Reference
Ravelli, R.B.G., Leiros, H.-K.S., Pan, B., Caffrey, M., McSweeney, S.: (2003) "Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures." Structure, 11, 217-224.
Abstract
The use of third generation synchrotron sources has led to renewed concern about the effect of ionizing radiation on crystalline biological samples. In general, the problem is seen as one to be avoided. However, in this paper, it is shown that, far from being a hindrance to successful structure determination, radiation damage provides an opportunity for phasing macromolecular structures. This is successfully demonstrated for both a protein and an oligonucleotide, by way of which complete models were built automatically. The possibility that, through the exploitation of radiation damage, the phase problem could become less of a barrier to macromolecular crystal structure determination is discussed.
G4 notes
6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 5'/5'-SEPARATED

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.098 type=planar nts=4 gggg A.BGM2,C.BGM2,H.BGM2,D.BGM2
 2 glyco-bond=---- groove=---- planarity=0.151 type=planar nts=4 GGGG A.G4,C.G4,H.G4,D.G4
 3 glyco-bond=---- groove=---- planarity=0.264 type=bowl   nts=4 GGGG A.G5,C.G5,H.G5,D.G5
 4 glyco-bond=---- groove=---- planarity=0.082 type=planar nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2
 5 glyco-bond=---- groove=---- planarity=0.154 type=planar nts=4 GGGG B.G4,E.G4,F.G4,G.G4
 6 glyco-bond=---- groove=---- planarity=0.257 type=bowl   nts=4 GGGG B.G5,E.G5,F.G5,G.G5

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4
 3  glyco-bond=---- groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,H.BGM2,C.BGM2
 4  glyco-bond=---- groove=---- WC-->Major nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G4,G.G4,F.G4,E.G4
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G5,G.G5,F.G5,E.G5
  step#1  mp(<<,backward) area=14.18 rise=3.64 twist=21.9
  step#2  mp(<<,backward) area=0.00  rise=6.68 twist=149.2
  step#3  mm(<>,outward)  area=31.43 rise=3.40 twist=-15.3
  step#4  pm(>>,forward)  area=0.00  rise=6.67 twist=-31.2
  step#5  pm(>>,forward)  area=13.66 rise=3.62 twist=22.6
  strand#1 RNA glyco-bond=------ nts=6 GGggGG A.G5,A.G4,A.BGM2,B.BGM2,B.G4,B.G5
  strand#2 RNA glyco-bond=------ nts=6 GGggGG C.G5,C.G4,D.BGM2,E.BGM2,G.G4,G.G5
  strand#3 RNA glyco-bond=------ nts=6 GGggGG H.G5,H.G4,H.BGM2,F.BGM2,F.G4,F.G5
  strand#4 RNA glyco-bond=------ nts=6 GGggGG D.G5,D.G4,C.BGM2,G.BGM2,E.G4,E.G5

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4
step#1 mp(<<,backward) area=14.18 rise=3.64 twist=21.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4
3 glyco-bond=---- groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,H.BGM2,C.BGM2
step#2 mp(<<,backward) area=0.00 rise=6.68 twist=149.2

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 3  glyco-bond=---- groove=---- Major-->WC nts=4 gggg A.BGM2,D.BGM2,H.BGM2,C.BGM2
4 glyco-bond=---- groove=---- WC-->Major nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2
step#3 mm(<>,outward) area=31.43 rise=3.40 twist=-15.3

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 4  glyco-bond=---- groove=---- WC-->Major nts=4 gggg B.BGM2,E.BGM2,F.BGM2,G.BGM2
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G4,G.G4,F.G4,E.G4
step#4 pm(>>,forward) area=0.00 rise=6.67 twist=-31.2

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G4,G.G4,F.G4,E.G4
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.G5,G.G5,F.G5,E.G5
step#5 pm(>>,forward) area=13.66 rise=3.62 twist=22.6

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List of 2 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G4,C.G4,H.G4,D.G4
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G5,C.G5,H.G5,D.G5
  step#1  pm(>>,forward)  area=14.18 rise=3.64 twist=21.9
  strand#1  U RNA glyco-bond=-- nts=2 GG A.G4,A.G5
  strand#2  U RNA glyco-bond=-- nts=2 GG C.G4,C.G5
  strand#3  U RNA glyco-bond=-- nts=2 GG H.G4,H.G5
  strand#4  U RNA glyco-bond=-- nts=2 GG D.G4,D.G5

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Stem#2, 2 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G4,E.G4,F.G4,G.G4
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.G5,E.G5,F.G5,G.G5
  step#1  pm(>>,forward)  area=13.66 rise=3.62 twist=22.6
  strand#1  U RNA glyco-bond=-- nts=2 GG B.G4,B.G5
  strand#2  U RNA glyco-bond=-- nts=2 GG E.G4,E.G5
  strand#3  U RNA glyco-bond=-- nts=2 GG F.G4,F.G5
  strand#4  U RNA glyco-bond=-- nts=2 GG G.G4,G.G5

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5'-SEPARATED]

List of 0 non-stem G4-loops (including the two closing Gs)