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PDBsum entry 1lcd
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Gene regulation/DNA
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PDB id
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1lcd
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Contents |
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* Residue conservation analysis
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J Mol Biol
234:446-462
(1993)
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PubMed id:
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Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics.
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V.P.Chuprina,
J.A.Rullmann,
R.M.Lamerichs,
J.H.van Boom,
R.Boelens,
R.Kaptein.
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ABSTRACT
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The structure of the complex of lac repressor headpiece and an 11 base-pair lac
half-operator has been determined by NMR spectroscopy and restrained Molecular
Dynamics calculations. In total 508 distances were derived from two-dimensional
nuclear Overhauser enhancement measurements, 260 of which are within the
headpiece, 212 within the operator and 36 between operator and headpiece. An
equilibrium restrained Molecular Dynamics calculation of the complex in aqueous
solution, spanning 85 picoseconds, has been used to analyze the structure.
Configuration sampling by an annealing procedure has been undertaken as well in
order to estimate the precision of the structure determination. Our data confirm
the results of previous two-dimensional NMR studies that the orientation of the
recognition helix of lac repressor in the major groove of DNA with respect to
the operator dyad axis is opposite to the orientation found in complexes of
other DNA binding proteins of the helix-turn-helix class. We find a number of
tight contacts between the protein and the operator that are in agreement with
the available genetic and biochemical data. The anchoring of lac headpiece on
the operator is similar to that of other repressors. Other features are unique
for lac headpiece: relative few direct hydrogen bonds between side-chains and
bases; extensive apolar contacts; many direct and water-bridged contacts to
phosphates from residues in or close to the recognition helix. Overall, an
interconnected set of interactions is observed, involving base-specific
contacts, phosphate contacts, intra-protein and water-bridged hydrogen bonds.
Several of these interactions appear to be dynamic, i.e. fluctuating in time,
rather than static.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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M.Lewis
(2011).
A tale of two repressors.
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J Mol Biol,
409,
14-27.
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T.Ohyama,
M.Hayakawa,
S.Nishikawa,
and
N.Kurita
(2011).
Specific interactions between lactose repressor protein and DNA affected by ligand binding: Ab initio molecular orbital calculations.
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J Comput Chem,
32,
1661-1670.
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M.van Dijk,
and
A.M.Bonvin
(2010).
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
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Nucleic Acids Res,
38,
5634-5647.
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J.Xu,
and
K.S.Matthews
(2009).
Flexibility in the inducer binding region is crucial for allostery in the Escherichia coli lactose repressor.
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Biochemistry,
48,
4988-4998.
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M.Taraban,
H.Zhan,
A.E.Whitten,
D.B.Langley,
K.S.Matthews,
L.Swint-Kruse,
and
J.Trewhella
(2008).
Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein.
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J Mol Biol,
376,
466-481.
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S.Mazier,
S.Villette,
S.Goffinont,
S.Renouard,
J.C.Maurizot,
D.Genest,
and
M.Spotheim-Maurizot
(2008).
Radiation damage to a DNA-binding protein. Combined circular dichroism and molecular dynamics simulation analysis.
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Radiat Res,
170,
604-612.
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K.Yamasaki,
T.Akiba,
T.Yamasaki,
and
K.Harata
(2007).
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.
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Nucleic Acids Res,
35,
5073-5084.
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PDB codes:
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M.van Dijk,
A.D.van Dijk,
V.Hsu,
R.Boelens,
and
A.M.Bonvin
(2006).
Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility.
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Nucleic Acids Res,
34,
3317-3325.
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N.Gillard,
M.Spotheim-Maurizot,
and
M.Charlier
(2005).
Radiation abolishes inducer binding to lactose repressor.
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Radiat Res,
163,
433-446.
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R.Kopke Salinas,
G.E.Folkers,
A.M.Bonvin,
D.Das,
R.Boelens,
and
R.Kaptein
(2005).
Altered specificity in DNA binding by the lac repressor: a mutant lac headpiece that mimics the gal repressor.
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Chembiochem,
6,
1628-1637.
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PDB code:
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T.Carlomagno
(2005).
Ligand-target interactions: what can we learn from NMR?
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Annu Rev Biophys Biomol Struct,
34,
245-266.
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C.G.Kalodimos,
A.M.Bonvin,
R.K.Salinas,
R.Wechselberger,
R.Boelens,
and
R.Kaptein
(2002).
Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.
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EMBO J,
21,
2866-2876.
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PDB code:
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L.Swint-Kruse,
C.Larson,
B.M.Pettitt,
and
K.S.Matthews
(2002).
Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR.
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Protein Sci,
11,
778-794.
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T.de Beer,
J.Fang,
M.Ortega,
Q.Yang,
L.Maes,
C.Duffy,
N.Berton,
J.Sippy,
M.Overduin,
M.Feiss,
and
C.E.Catalano
(2002).
Insights into specific DNA recognition during the assembly of a viral genome packaging machine.
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Mol Cell,
9,
981-991.
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PDB code:
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B.Dubertret,
S.Liu,
Q.Ouyang,
and
A.Libchaber
(2001).
Dynamics of DNA-protein interaction deduced from in vitro DNA evolution.
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Phys Rev Lett,
86,
6022-6025.
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C.E.Bell,
and
M.Lewis
(2001).
The Lac repressor: a second generation of structural and functional studies.
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Curr Opin Struct Biol,
11,
19-25.
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L.Swint-Kruse,
C.R.Elam,
J.W.Lin,
D.R.Wycuff,
and
K.Shive Matthews
(2001).
Plasticity of quaternary structure: twenty-two ways to form a LacI dimer.
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Protein Sci,
10,
262-276.
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P.C.Ng,
and
S.Henikoff
(2001).
Predicting deleterious amino acid substitutions.
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Genome Res,
11,
863-874.
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E.d'Alençon,
and
S.D.Ehrlich
(2000).
A study of the CopF repressor of plasmid pAMbeta1 by phage display.
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J Bacteriol,
182,
2973-2977.
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C.A.Spronk,
A.M.Bonvin,
P.K.Radha,
G.Melacini,
R.Boelens,
and
R.Kaptein
(1999).
The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator.
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Structure,
7,
1483-1492.
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PDB code:
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C.A.Spronk,
G.E.Folkers,
A.M.Noordman,
R.Wechselberger,
N.van den Brink,
R.Boelens,
and
R.Kaptein
(1999).
Hinge-helix formation and DNA bending in various lac repressor-operator complexes.
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EMBO J,
18,
6472-6480.
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C.M.Falcon,
and
K.S.Matthews
(1999).
Glycine insertion in the hinge region of lactose repressor protein alters DNA binding.
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J Biol Chem,
274,
30849-30857.
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I.Ohki,
N.Shimotake,
N.Fujita,
M.Nakao,
and
M.Shirakawa
(1999).
Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1.
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EMBO J,
18,
6653-6661.
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PDB code:
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K.Nadassy,
S.J.Wodak,
and
J.Janin
(1999).
Structural features of protein-nucleic acid recognition sites.
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Biochemistry,
38,
1999-2017.
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C.R.Robinson,
and
S.G.Sligar
(1998).
Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease.
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Proc Natl Acad Sci U S A,
95,
2186-2191.
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L.Swint-Kruse,
K.S.Matthews,
P.E.Smith,
and
B.M.Pettitt
(1998).
Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P.
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Biophys J,
74,
413-421.
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M.D.Allen,
K.Yamasaki,
M.Ohme-Takagi,
M.Tateno,
and
M.Suzuki
(1998).
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
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EMBO J,
17,
5484-5496.
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PDB codes:
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M.Gerstein,
and
W.Krebs
(1998).
A database of macromolecular motions.
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Nucleic Acids Res,
26,
4280-4290.
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R.J.Keenan,
D.M.Freymann,
P.Walter,
and
R.M.Stroud
(1998).
Crystal structure of the signal sequence binding subunit of the signal recognition particle.
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Cell,
94,
181-191.
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PDB code:
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A.V.Kralicek,
P.K.Wilson,
G.B.Ralston,
R.G.Wake,
and
G.F.King
(1997).
Reorganization of terminator DNA upon binding replication terminator protein: implications for the functional replication fork arrest complex.
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Nucleic Acids Res,
25,
590-596.
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C.M.Falcon,
L.Swint-Kruse,
and
K.S.Matthews
(1997).
Designed disulfide between N-terminal domains of lactose repressor disrupts allosteric linkage.
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J Biol Chem,
272,
26818-26821.
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H.Backes,
C.Berens,
V.Helbl,
S.Walter,
F.X.Schmid,
and
W.Hillen
(1997).
Combinations of the alpha-helix-turn-alpha-helix motif of TetR with respective residues from LacI or 434Cro: DNA recognition, inducer binding, and urea-dependent denaturation.
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Biochemistry,
36,
5311-5322.
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J.G.Omichinski,
P.V.Pedone,
G.Felsenfeld,
A.M.Gronenborn,
and
G.M.Clore
(1997).
The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode.
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Nat Struct Biol,
4,
122-132.
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PDB codes:
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J.H.Kim,
and
G.H.Chambliss
(1997).
Contacts between Bacillus subtilis catabolite regulatory protein CcpA and amyO target site.
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Nucleic Acids Res,
25,
3490-3496.
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L.Li,
and
K.S.Matthews
(1997).
Differences in water release with DNA binding by ultrabithorax and deformed homeodomains.
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Biochemistry,
36,
7003-7011.
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M.A.Kercher,
P.Lu,
and
M.Lewis
(1997).
Lac repressor-operator complex.
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Curr Opin Struct Biol,
7,
76-85.
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M.Lopata,
D.Schlieper,
B.von Wilcken-Bergmann,
and
B.Müller-Hill
(1997).
A lethal mutant of the catabolite gene activator protein CAP of Escherichia coli.
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Biol Chem,
378,
1153-1162.
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M.Slijper,
R.Boelens,
A.L.Davis,
R.N.Konings,
G.A.van der Marel,
J.H.van Boom,
and
R.Kaptein
(1997).
Backbone and side chain dynamics of lac repressor headpiece (1-56) and its complex with DNA.
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Biochemistry,
36,
249-254.
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C.A.Spronk,
M.Slijper,
J.H.van Boom,
R.Kaptein,
and
R.Boelens
(1996).
Formation of the hinge helix in the lac repressor is induced upon binding to the lac operator.
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Nat Struct Biol,
3,
916-919.
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H.Thorogood,
T.R.Waters,
A.W.Parker,
C.W.Wharton,
and
B.A.Connolly
(1996).
Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.
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Biochemistry,
35,
8723-8733.
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J.D.Gralla
(1996).
Activation and repression of E. coli promoters.
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Curr Opin Genet Dev,
6,
526-530.
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J.G.McAfee,
S.P.Edmondson,
I.Zegar,
and
J.W.Shriver
(1996).
Equilibrium DNA binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: fluorescence and circular dichroism studies.
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Biochemistry,
35,
4034-4045.
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J.H.Miller
(1996).
Structure of a paradigm.
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Nat Struct Biol,
3,
310-312.
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P.G.Artz,
K.G.Valentine,
S.J.Opella,
and
P.Lu
(1996).
Lac repressor-operator interaction: N-terminal peptide backbone 1H and 15N chemical shifts upon complex formation with DNA.
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J Mol Recognit,
9,
13-22.
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R.T.Sauer
(1996).
Lac repressor at last.
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Structure,
4,
219-222.
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A.Nagadoi,
S.Morikawa,
H.Nakamura,
M.Enari,
K.Kobayashi,
H.Yamamoto,
G.Sampei,
K.Mizobuchi,
M.A.Schumacher,
and
R.G.Brennan
(1995).
Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain.
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Structure,
3,
1217-1224.
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PDB codes:
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H.C.van Leeuwen,
M.J.Strating,
M.Cox,
R.Kaptein,
and
P.C.van der Vliet
(1995).
Mutation of the Oct-1 POU-specific recognition helix leads to altered DNA binding and influences enhancement of adenovirus DNA replication.
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Nucleic Acids Res,
23,
3189-3197.
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R.Kaptein,
M.Slijper,
and
R.Boelens
(1995).
Structure and dynamics of the lac repressor-operator complex as determined by NMR.
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Toxicol Lett,
82,
591-599.
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R.T.Sauer
(1995).
Minor groove DNA-recognition by alpha-helices.
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Nat Struct Biol,
2,
7-9.
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S.Oehler,
M.Amouyal,
P.Kolkhof,
B.von Wilcken-Bergmann,
and
B.Müller-Hill
(1994).
Quality and position of the three lac operators of E. coli define efficiency of repression.
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EMBO J,
13,
3348-3355.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
