Supplementary information
1. In addition to this biologically relevant dimer, a metal-tethered dimer, which was first described in the apo and
drug-bound structures of BRC14, is found between crystallographic symmetry mates. In the crystals of
BmrRTPPDNA complex, this metal-tethered interface allows formation of an infinite array of dimers.
However, neither the nature of the metal nor the biological significance of this metal-dependent oligomerization,
if any, is known.
2. A large tetrahedral electron density feature for TPP molecule was found at the interface between
crystallographic symmetry mates. Residues Tyr5, Tyr35 and Tyr44 from one BmrR molecule and Phe230 from
its symmetry mate create this fortuitous binding site. TPP likely serves as a crystallization agent, since crystals
do not appear in the presence of any other drug under this crystallization condition.
3. An overlay of the C atoms of residues 122-144, 169-194, 204-258, and 268-277 of BmrR onto the
corresponding C atoms of the apo and drug-bound BRC results in r.m.s.d. of 0.61 Å and 0.64 Å, respectively.
Table 1 Crystallographic statistics
Native
Data collection
All data
Resolution (Å)
87.2-3.0
Total observations
55,012
Unique reflections
16,127
Completeness (%)
88
Overall I/(I)
5.5
Rmerge*(%)
9.4
Highest resolution shell
Resolution (Å)
3.1-3.0
Completeness (%)
65
I/(I)
2.2
Rmerge (%)
27.5
Multiple isomorphous replacement
Riso† (%)
Number of sites
Rcullis‡
Phasing power§
Overall figure of merit|| is 0.44 to 3.0 Å
Refinement
Resolution (Å)
Reflections
Completeness, %
Protein atoms
DNA atoms
TPP/TPSb atoms
Solvent molecules
Rfactor/Rfree ¶, %
r.m.s. deviations
Bond length (Å)
Bond angles (˚)
B-factor (Å2)
thimerosal
K2PtCl4 iodo1
TPSb
88.0-3.0
53,690
16,509
90
10.0
9.6
51.7-3.05
35,853
14,603
78
5.0
10.8
87.3-3.0
50,511
16,224
89
6.0
7.6
60.4-3.12
44,719
14,141
86
3.7
12.0
3.1-3.0
71
2.1
27.8
3.15-3.05
58
2.1
25.5
3.1-3.0
73
2.1
24.8
3.6-3.12
78
2.1
27.8
9.6
0.5
0.60
1.44
10.1
1
0.65
1.19
6.3
1
0.65
1.02
16.0-3.0
15,978
88.0
2,098
427
25
6
24.0/31.5
16.0-3.12
14,001
86.0
2,112
427
50
3
26.8/31.7
0.014
1.50
3.89
0.015
1.50
N/A
PROCHECK28: Residues in Ramachandran regions, % (number of residues)
most favourable
75.1 (190)
allowed
22.9 (58)
generously allowed
2.0 (5)
75.1 (190)
23.3 (59)
1.6 (4)
*Rmerge = ∑∑|Ihkl-Ihkl(j)|/ ∑NIhkl, where Ihkl(j) is observed intensity and Ihkl is the final average value of
intensity. †Riso = ∑||FPH|-|FP||/∑||FP|+|FPH||, where |FP| is the protein structure factor amplitude and |FPH| is the
heavy atom derivative structure factor amplitude. ‡Rcullis = ∑||FPH±FP|-FH(calc)|/∑|FPH±FP|. §Phasing power is
[∑|FPH(calc)|2/∑{|FPH(obs)|-|FPH(calc)|}2]1/2. ||Figure of merit is <|∑P()ei/∑P()|>, where  is the phase and P() is
the phase probability distribution. ¶Rfactor = ∑||Fobs|-|Fcalc||/∑|Fobs|. Rfree is calculated for 5% of all reflections,
excluded from refinement. Data for the highest resolution shells are shown in parentheses. NA stands for "not
applicable".
a
Duplex DNA (unbound)
5'AGACT6CT1CCCCT2A GGAGGA GGTC
·
3'CTGA GA GGGGA T5CCTCCT3CCAGT
b
BmrRTPP bound bmr DNA
13' 12' 11' 10' 9'
8' 7'
6
6'
5' 4' 3' 2'
1'
1
1
2
3 4 5
6 7
8
9 10 11
2
AGACT CT CCCCT AGGAGGA GGTC
·
CTGA GA GGGGAT5 CCTCCT3CCAGT
12 11 10 9
c
8 7
6
5 4
3 2
1
1' 2' 3'
4' 5' 6' 7'
8' 9' 10' 11' 12'
Experimentally fit DNA sequence
11' 10' 9' 8' 7' 6' 5' 4' 3' 2' 1' 1 2
3 4
5 6 7
8
9 10 11
ACCCTCCCCT TAGGGGAGGGT
·
TGGGAGGGGAT TCCCCTCCCA
11 10 9 8
7
6 5
4 3 2
1
1' 2' 3' 4' 5' 6' 7' 8' 9' 10' 11'
Zheleznova & Brennan, SI, Fig. 1
Figure 1. Sequences of the bmr operator duplex used in this work. a, Pseudopalindromic unbound operator
DNA. b, Pseudopalindromic BmrR·TPP-bound operator DNA. c, BmrR·TPP-bound operator. The unique
half-site, which is the best fit of the electron density and is used in refinement, is shown in magenta. The DNA
pseudo dyad (a, b) and crystallographic dyad (c) axes are shown as dots. Identical bases on either side of the
dyad are shown in bold (a, b). Locations of iodine sites are indicated using superscripted numbers.
Figure 2. Sequence alignment of selected MerR family proteins. The secondary structure elements of BmrR are
indicated above the sequence by arrows for  strands and rods for  helices. The colour code of the secondary
structure is the same as in Fig. 2a, main text. The sequence is coloured to show identical (red) and conserved
(yellow) residues of the DNA-binding domain. Marked are BmrR residues that contact the DNA using side
chain and main chain atoms (black triangles) or only main chain atoms (blue triangles). The hydrogen-bond
acceptor at position 26 is marked with a green triangle. Acidic residues of the multidrug-binding pocket are
marked with red circles. Cysteines of MerR and SoxR involved in binding Hg2+ ion and 2Fe-2S redox centres,
respectively, are boxed in magenta and blue. The sequence alignment was done using ALSCRIPT (Barton, G.J.
ALSCRIPT: a tool to format multiple sequence alignments. Prot. Eng. 6, 37-40 (1993).
2