Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR
Maria A.Schumacher, Marshall C.Miller, Steve Grkovic, Melissa H.Brown, Ronald A.Skurray and Richard G.Brennan
The EMBO Journal, 21, 1210–1218, 2002
In the above paper, some of the cell constants were printed incorrectly in Table I. The correct version should read:
Table I. QacR–DNA structure determination and refinement.
| Crystal | Native 2 | Native 1 | io13 | io12′/8′ | io2 | io3 | Dy/io2 | Uranyl |
|---|---|---|---|---|---|---|---|---|
| Space group | P65 | P65 | P65 | P65 | P65 | P65 | P65 | P65 |
| Cell constants (Å) | ||||||||
| a | 174.7 | 174.0 | 174.7 | 175.0 | 174.5 | 174.0 | 174.6 | 175.3 |
| b | 174.7 | 174.0 | 174.7 | 175.0 | 174.5 | 174.0 | 174.6 | 175.3 |
| c | 152.0 | 152.1 | 151.0 | 152.9 | 151.6 | 151.1 | 151.5 | 153.2 |
| Resolution (Å) | 2.90 | 3.35 | 3.70 | 4.60 | 3.70 | 4.70 | 3.70 | 4.80 |
| Overall Rsym (%)a | 5.4 | 9.9 | 9.7 | 10.9 | 5.0 | 11.4 | 10.7 | 11.5 |
| Overall I/σ(I) | 11.4 | 10.5 | 12.2 | 10.3 | 13.5 | 9.8 | 11.5 | 14.6 |
| High resolution (Å) | 3.03–2.90 | 3.5–3.35 | 4.1–3.7 | 5.4–3.6 | 4.1–3.7 | 5.4–4.7 | 4.1–3.7 | 5.5–4.8 |
| Rsym (%) | 40.1 | 24.9 | 21.0 | 35.5 | 12.3 | 15.0 | 25.2 | 25.0 |
| I/σ(I) | 1.8 | 1.3 | 2.7 | 2.0 | 2.3 | 2.8 | 1.9 | 2.3 |
| Total reflections (No.) | 302 270 | 85 618 | 58 289 | 96 855 | 55 213 | 71 643 | 35 842 | 64 543 |
| Unique reflections (No.) | 59 396 | 39 618 | 26 650 | 22 516 | 27 646 | 23 102 | 26 450 | 21 610 |
| Phasing powerb | 0.81 | 0.95 | 1.19 | 0.84 | 1.02 | 1.00 | ||
| Rcullisc | 0.629 | 0.704 | 0.718 | 0.697 | 0.690 | 0.636 | ||
| Riso (%)d | 8.5 | 10.6 | 9.1 | 9.5 | 10.5 | 17.7 | ||
| Heavy atom sites (No.) | 2 | 4 | 2 | 2 | 4 | 4 | ||
| Overall figure of merite |
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0.42 |
| Refinement statistics: native 2 | ||||||||
| Completeness (%) | 98.7 | |||||||
| Resolution (Å) | 75.70–2.90 | |||||||
| Rwork/Rfree (%)f | 22.2/25.8 | |||||||
| R.m.s.d. | ||||||||
| Bond angles (°) | 1.36 | |||||||
| Bond lengths (Å) | 0.009 | |||||||
| B-values (Å2) | 2.5 | |||||||
| Solvent (No., water/sulfate) | 45/5 | |||||||
| Ramachandran analysis | ||||||||
| Most favored (%/No.) | 86.5/610 | |||||||
| Additionally allowed (%/No.) | 12.8/90 | |||||||
| Generously allowed (%/No.) | 0.1/1 | |||||||
| Disallowed (%/No.) | 0.6/4 | |||||||
aRsym = ΣΣ|Ihkl – Ihkl(j)|/ΣIhkl, where Ihkl(j) is the observed intensity and Ihkl is the final average value of intensity.
bPhasing power = r.m.s. (|Fh|/E), where |Fh| is the heavy atom structure factor amplitude and E is the residual lack of closure error.
cRCullis = Σ||Fh(obs)| – |Fh(calc)||/Σ|Fh(obs)| for centric reflections, where |Fh(obs)| is the observed heavy atom structure factor amplitudes and |Fh(calc)| is the calculated heavy atom structure factor amplitude.
dRiso = Σ||Fph| – |Fp||/Σ|Fp|, where |Fp| is the protein structure factor amplitude and |Fph| is the heavy atom derivative structure factor amplitude.
eFigure of merit = <|ΣP(α)eiα/ΣP(α)|>, where α is the phase and P(α) is the phase probability distribution.
fRwork = Σ||Fobs| – |Fcalc||/Σ|Fobs| and Rfree = Σ||Fobs| – |Fcalc||/Σ|Fobs|, where all reflections belong to a test set of 10% data randomly selected in CNS.
The ‘io’ designator indicates the locations of the 5-iodouracil substitutions numbered in Figure 1A. ‘io12′/8′’ is a double 5-iodouracil-substituted oligodeoxynucleotide. ‘Dy’ and ‘Uranyl’ indicate dysprosium chloride and uranyl acetate, respectively.
The publisher would like to apologize for this error and any confusion caused.