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Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence
Authors
Kalodimos, C., Bonvin, A., Boelens, R., Kaptein, R.
Assembly
Lactose operon repressor
Entity
1. Lactose operon repressor (polymer, Thiol state: all disulfide bound), 62 monomers, 6814.688 × 2 Da Detail

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL


2. Binding DNA (polymer, Thiol state: not present), 9 monomers, 2826.821 Da Detail

CGATAAGAT


3. Binding DNA (polymer, Thiol state: not present), 9 monomers, 2768.769 Da Detail

ATCTTATCG


Total weight
19224.967 Da
Max. entity weight
6814.688 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
THE STRUCTURE OF THE COMPLEX WAS CALCULATED AS FOLLOWS. FIRST THE STRUCTURE OF THE DIMERIC LACHP62-V52C WAS CALCULATED USING ONLY PROTEIN NMR RESTRAINTS. THE 100 BEST STRUCTURES WERE SELECTED AND DOCKED ONTO THE NONSPECIFIC LAC OPERATOR B-DNA USING SIMULATED ANNEALING. DISTANCE AND PLANARITY RESTRAINTS FOR THE DNA WERE INCORPORATED IN ORDER TO KEEP DNA CLOSE TO B-DNA CONFORMATION.
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 76.2 %, Completeness: 60.5 %, Completeness (bb): 59.8 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All60.5 % (532 of 879)63.9 % (343 of 537)43.9 % (119 of 271)98.6 % (70 of 71)
Backbone59.8 % (294 of 492)47.6 % (118 of 248)63.6 % (117 of 184)98.3 % (59 of 60)
Sidechain53.2 % (238 of 447)77.9 % (225 of 289) 1.4 % (2 of 147)100.0 % (11 of 11)
Aromatic25.0 % (18 of 72)33.3 % (18 of 54) 0.0 % (0 of 18)
Methyl48.8 % (40 of 82)86.4 % (38 of 44) 5.3 % (2 of 38)

1. Lactose operon repressor

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. Binding DNA

CGATAAGAT

3. Binding DNA

ATCTTATCG

Sample

Pressure 1 atm, Temperature 300 K, pH 5.8


#NameIsotope labelingTypeConcentration
1Lactose operon repressor[U-15N; U-13C]4 mM
2Binding DNA[U-15N; U-13C]2 mM
3Binding DNA[U-15N; U-13C]2 mM
4KPI60 mM
5KCL400 mM
6H2O90 %
7D2O10 %

Chem. Shift Complete2
Sequence coverage: 11.2 %, Completeness: 34.6 %, Completeness (bb): 36.1 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All34.6 % (608 of 1758)39.0 % (419 of 1074)22.0 % (119 of 542)49.3 % (70 of 142)
Backbone36.1 % (355 of 984)36.1 % (179 of 496)31.8 % (117 of 368)49.2 % (59 of 120)
Sidechain28.3 % (253 of 894)41.5 % (240 of 578) 0.7 % (2 of 294)50.0 % (11 of 22)
Aromatic21.5 % (31 of 144)28.7 % (31 of 108) 0.0 % (0 of 36)
Methyl25.6 % (42 of 164)45.5 % (40 of 88) 2.6 % (2 of 76)

1. Lactose operon repressor

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. Binding DNA

CGATAAGAT

3. Binding DNA

ATCTTATCG

Sample

Pressure 1 atm, Temperature 300 K, pH 5.8


#NameIsotope labelingTypeConcentration
1Lactose operon repressor[U-15N; U-13C]4 mM
2Binding DNA[U-15N; U-13C]2 mM
3Binding DNA[U-15N; U-13C]2 mM
4KPI60 mM
5KCL400 mM
6H2O90 %
7D2O10 %

Chem. Shift Complete3
Sequence coverage: 11.2 %, Completeness: 25.6 %, Completeness (bb): 27.4 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All25.6 % (675 of 2637)30.2 % (486 of 1611)14.6 % (119 of 813)32.9 % (70 of 213)
Backbone27.4 % (405 of 1476)30.8 % (229 of 744)21.2 % (117 of 552)32.8 % (59 of 180)
Sidechain20.1 % (270 of 1341)29.6 % (257 of 867) 0.5 % (2 of 441)33.3 % (11 of 33)
Aromatic20.4 % (44 of 216)27.2 % (44 of 162) 0.0 % (0 of 54)
Methyl18.7 % (46 of 246)33.3 % (44 of 132) 1.8 % (2 of 114)

1. Lactose operon repressor

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. Binding DNA

CGATAAGAT

3. Binding DNA

ATCTTATCG

Sample

Pressure 1 atm, Temperature 300 K, pH 5.8


#NameIsotope labelingTypeConcentration
1Lactose operon repressor[U-15N; U-13C]4 mM
2Binding DNA[U-15N; U-13C]2 mM
3Binding DNA[U-15N; U-13C]2 mM
4KPI60 mM
5KCL400 mM
6H2O90 %
7D2O10 %

Protein Blocks Logo
Calculated from 20 models in PDB: 1OSL, Strand ID: A, B Detail


Release date
2004-10-17
Citation
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
Kalodimos, C., Biris, N., Bonvin, A.M., Levandoski, M.M., Guennuegues, M., Boelens, R., Kaptein, R.
Science (2004), 305, 386-389, PubMed 15256668 , DOI 10.1126/science.1097064 ,
Related entities 1. Lactose operon repressor, : 1 : 4 : 15 : 146 entities Detail
Experiments performed 3 experiments Detail
Keywords Protein-DNA complex, Lac repressor, nonspecific interaction