PDBsum entry 1ick

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dna_rna ligands metals links
Waters ×89
PDB id:
Name: DNA
Title: Left-handed z-DNA hexamer duplex d(cgcgcg)2
Structure: 5'-d( Cp Gp Cp Gp Cp G)-3'. Chain: a, b. Engineered: yes
Source: Synthetic: yes
0.95Å     R-factor:   0.086    
Authors: Z.Dauter,D.A.Adamiak
Key ref:
Z.Dauter and D.A.Adamiak (2001). Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy. Acta Crystallogr D Biol Crystallogr, 57, 990-995. PubMed id: 11418767 DOI: 10.1107/S0907444901006382
01-Apr-01     Release date:   12-Apr-01    


DOI no: 10.1107/S0907444901006382 Acta Crystallogr D Biol Crystallogr 57:990-995 (2001)
PubMed id: 11418767  
Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.
Z.Dauter, D.A.Adamiak.
The crystal structure of a left-handed Z-DNA hexamer duplex d(CGCGCG)(2) has been solved based on the anomalous diffraction signal of inherent P atoms using data collected at the single wavelength of 1.54 A. The anomalous signal of about 2% of the total diffracted intensity, constant for all nucleic acids, may be generally useful for solving crystal structures of DNA and RNA oligomers. The multiplicity of intensity measurements is shown to crucially affect the data quality and the ability to solve the phase problem. The anisotropic model refined to an R factor of 8.9% at 0.95 A resolution.
  Selected figure(s)  
Figure 2.
Figure 2 Experimental solvent-flattened electron-density maps at 1.5 resolution plotted at the 1 level and calculated for the four long-wavelength data sets: (a, b) L360, (c) L270, (d) L180 and (e) L90. This figure was prepared with BOBSCRIPT (Esnouf, 1999[Esnouf, R. M. (1999). Acta Cryst. D55, 938-940.]).
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 990-995) copyright 2001.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21280021 H.E.Peckham, and W.K.Olson (2011).
Nucleic-acid structural deformability deduced from anisotropic displacement parameters.
  Biopolymers, 95, 254-269.  
21481775 T.D.Fenn, M.J.Schnieders, M.Mustyakimov, C.Wu, P.Langan, V.S.Pande, and A.T.Brunger (2011).
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
  Structure, 19, 523-533.
PDB code: 3qba
17637337 A.Y.Keel, R.P.Rambo, R.T.Batey, and J.S.Kieft (2007).
A general strategy to solve the phase problem in RNA crystallography.
  Structure, 15, 761-772.
PDB codes: 2pxb 2pxd 2pxe 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv
12445769 J.Choe, S.Suresh, G.Wisedchaisri, K.J.Kennedy, M.H.Gelb, and W.G.Hol (2002).
Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase.
  Chem Biol, 9, 1189-1197.
PDB codes: 1jdj 1m66 1m67 1n1g
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