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Assignment of lac repressor headpiece complexed of its natural operator
Authors
Kalodimos, C.G., Bonvin, A.J.M.M., Salinas, R.K., Wechselberger, R., Boelens, R., Kaptein, R.
Assembly
LACTOSE OPERON REPRESSOR/DNA Complex
Entity
1. lactose repressor-operator (polymer, Thiol state: all disulfide bound), 62 monomers, 6814.688 × 2 Da Detail

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL


2. lactose repressor-operator DNA (polymer, Thiol state: not present), 23 monomers, 7206.616 Da Detail

GAATTGTGAG CGGATAACAA TTT


3. lactose repressor-operator DNA (polymer, Thiol state: not present), 23 monomers, 7037.506 Da Detail

AAATTGTTAT CCGCTCACAA TTC


Total weight
27873.498 Da
Max. entity weight
7206.616 Da
Entity Connection
disulfide 1 Detail

IDTypeValue orderAtom ID 1Atom ID 2
1disulfidesing1:CYS52:SG1:CYS52:SG

Source organism
Escherichia coli
Exptl. method
NMR
Refine. method
SIMULATED ANNEALING FOLLOWED BY RESTRAINED MDR
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 56.5 %, Completeness: 56.0 %, Completeness (bb): 50.3 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All56.0 % (644 of 1150)42.6 % (344 of 808)86.0 % (233 of 271)94.4 % (67 of 71)
Backbone50.3 % (346 of 688)26.4 % (117 of 444)94.0 % (173 of 184)93.3 % (56 of 60)
Sidechain67.8 % (354 of 522)62.4 % (227 of 364)78.9 % (116 of 147)100.0 % (11 of 11)
Aromatic14.8 % (19 of 128)15.5 % (17 of 110)11.1 % (2 of 18)
Methyl82.4 % (75 of 91)71.7 % (38 of 53)97.4 % (37 of 38)

1. lactose repressor-operator

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. lactose repressor-operator DNA

GAATTGTGAG CGGATAACAA TTT

3. lactose repressor-operator DNA

AAATTGTTAT CCGCTCACAA TTC

Sample

Pressure 1 atm, Temperature 315 (±0.1) K, pH 6.0 (±0.1)


#NameIsotope labelingTypeConcentration
1lactose repressor-operator[U-15N; U-13C]4 mM
2lactose repressor-operator DNA2 mM
3lactose repressor-operator DNA2 mM
4KPi10 mM
5KCl20 mM
6D2O10 %
7H2O90 %

Chem. Shift Complete2
Sequence coverage: 55.6 %, Completeness: 55.7 %, Completeness (bb): 49.9 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All55.7 % (1281 of 2300)42.6 % (688 of 1616)84.9 % (460 of 542)93.7 % (133 of 142)
Backbone49.9 % (686 of 1376)26.2 % (233 of 888)92.9 % (342 of 368)92.5 % (111 of 120)
Sidechain67.5 % (705 of 1044)62.5 % (455 of 728)77.6 % (228 of 294)100.0 % (22 of 22)
Aromatic14.5 % (37 of 256)15.9 % (35 of 220) 5.6 % (2 of 36)
Methyl82.4 % (150 of 182)71.7 % (76 of 106)97.4 % (74 of 76)

1. lactose repressor-operator

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. lactose repressor-operator DNA

GAATTGTGAG CGGATAACAA TTT

3. lactose repressor-operator DNA

AAATTGTTAT CCGCTCACAA TTC

Sample

Pressure 1 atm, Temperature 315 (±0.1) K, pH 6.0 (±0.1)


#NameIsotope labelingTypeConcentration
1lactose repressor-operator[U-15N; U-13C]4 mM
2lactose repressor-operator DNA2 mM
3lactose repressor-operator DNA2 mM
4KPi10 mM
5KCl20 mM
6D2O10 %
7H2O90 %

Chem. Shift Complete3
Sequence coverage: 30.6 %, Completeness: 43.6 %, Completeness (bb): 40.4 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All43.6 % (1503 of 3450)36.1 % (875 of 2424)60.0 % (488 of 813)65.7 % (140 of 213)
Backbone40.4 % (834 of 2064)26.6 % (354 of 1332)65.6 % (362 of 552)65.6 % (118 of 180)
Sidechain50.2 % (786 of 1566)47.6 % (520 of 1092)55.3 % (244 of 441)66.7 % (22 of 33)
Aromatic19.8 % (76 of 384)22.4 % (74 of 330) 3.7 % (2 of 54)
Methyl64.5 % (176 of 273)57.9 % (92 of 159)73.7 % (84 of 114)

1. lactose repressor-operator

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. lactose repressor-operator DNA

GAATTGTGAG CGGATAACAA TTT

3. lactose repressor-operator DNA

AAATTGTTAT CCGCTCACAA TTC

Sample

Pressure 1 atm, Temperature 315 (±0.1) K, pH 6.0 (±0.1)


#NameIsotope labelingTypeConcentration
1lactose repressor-operator[U-15N; U-13C]4 mM
2lactose repressor-operator DNA2 mM
3lactose repressor-operator DNA2 mM
4KPi10 mM
5KCl20 mM
6D2O10 %
7H2O90 %

Chem. Shift Complete4
Sequence coverage: 41.7 %, Completeness: 40.0 %, Completeness (bb): 38.1 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All40.0 % (1838 of 4600)34.6 % (1117 of 3232)51.5 % (558 of 1084)57.4 % (163 of 284)
Backbone38.1 % (1048 of 2752)27.9 % (496 of 1776)56.1 % (413 of 736)57.9 % (139 of 240)
Sidechain44.3 % (924 of 2088)42.6 % (620 of 1456)47.6 % (280 of 588)54.5 % (24 of 44)
Aromatic23.0 % (118 of 512)26.4 % (116 of 440) 2.8 % (2 of 72)
Methyl57.1 % (208 of 364)51.4 % (109 of 212)65.1 % (99 of 152)

1. lactose repressor-operator

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. lactose repressor-operator DNA

GAATTGTGAG CGGATAACAA TTT

3. lactose repressor-operator DNA

AAATTGTTAT CCGCTCACAA TTC

Sample

Pressure 1 atm, Temperature 315 (±0.1) K, pH 6.0 (±0.1)


#NameIsotope labelingTypeConcentration
1lactose repressor-operator[U-15N; U-13C]4 mM
2lactose repressor-operator DNA2 mM
3lactose repressor-operator DNA2 mM
4KPi10 mM
5KCl20 mM
6D2O10 %
7H2O90 %

LACS Plot; CA
Referencing offset: -0.49 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: -0.49 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: 0.18 ppm, Outliers: 2 Detail
LACS Plot; CO
Referencing offset: -0.44 ppm, Outliers: 1 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 1L1M, Strand ID: A, B Detail


Release date
2002-06-06
Citation
Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain
Kalodimos, C.G., Bonvin, A.J.M.M., Salinas, R.K., Wechselberger, R., Boelens, R., Kaptein, R.
EMBO J. (2002), 21, 2866-2876, PubMed 12065400 , DOI 10.1093/emboj/cdf318 ,
Related entities 1. lactose repressor-operator, : 1 : 4 : 15 : 146 entities Detail
Experiments performed 3 experiments Detail
Keywords transcription regulation, LAC operon, LAC repressor, natural LAC operator, asymmetric DNA-binding, HTH