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BMRB: 5791


5791
1OSL
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: 75.0 %, Completeness: 59.1 %, Completeness (bb): 58.7 % Detail
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Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All59.1 % (518 of 876)61.8 % (332 of 537)45.0 % (122 of 271)94.1 % (64 of 68)
Backbone58.7 % (290 of 494)46.0 % (115 of 250)64.7 % (119 of 184)93.3 % (56 of 60)
Sidechain52.9 % (234 of 442)75.6 % (217 of 287) 6.1 % (9 of 147)100.0 % (8 of 8)
Aromatic25.0 % (18 of 72)33.3 % (18 of 54) 0.0 % (0 of 18)
Methyl50.0 % (41 of 82)81.8 % (36 of 44)13.2 % (5 of 38)

1. Lactose operon repressor

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. Binding DNA

CGATAAGAT

3. Binding DNA

ATCTTATCG

Show sample condition
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: 21.3 %, Completeness: 37.5 %, Completeness (bb): 39.6 % Detail
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Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All37.5 % (657 of 1752)41.0 % (440 of 1074)26.8 % (145 of 542)52.9 % (72 of 136)
Backbone39.6 % (391 of 988)38.0 % (190 of 500)37.5 % (138 of 368)52.5 % (63 of 120)
Sidechain31.7 % (280 of 884)43.6 % (250 of 574) 7.1 % (21 of 294)56.3 % (9 of 16)
Aromatic21.5 % (31 of 144)28.7 % (31 of 108) 0.0 % (0 of 36)
Methyl29.3 % (48 of 164)45.5 % (40 of 88)10.5 % (8 of 76)

1. Lactose operon repressor

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. Binding DNA

CGATAAGAT

3. Binding DNA

ATCTTATCG

Show sample condition
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: 18.8 %, Completeness: 29.8 %, Completeness (bb): 31.8 % Detail
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Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All29.8 % (784 of 2628)33.3 % (537 of 1611)20.8 % (169 of 813)38.2 % (78 of 204)
Backbone31.8 % (472 of 1482)33.2 % (249 of 750)28.1 % (155 of 552)37.8 % (68 of 180)
Sidechain25.0 % (332 of 1326)33.4 % (288 of 861) 7.7 % (34 of 441)41.7 % (10 of 24)
Aromatic20.4 % (44 of 216)27.2 % (44 of 162) 0.0 % (0 of 54)
Methyl22.8 % (56 of 246)34.8 % (46 of 132) 8.8 % (10 of 114)

1. Lactose operon repressor

MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RCAQQLAGKQ SL

2. Binding DNA

CGATAAGAT

3. Binding DNA

ATCTTATCG

Show sample condition
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 : 16 : 178 entities Detail
More details for 199 related entities
Experiments performed 3 experiments Detail
nullKeywords Protein-DNA complex, Lac repressor, nonspecific interaction