BMRB Entry 5791

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR5791
MolProbity Validation Chart

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Title:
Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence
Deposition date:
2003-05-01
Original release date:
2004-10-18
Authors:
Kalodimos, C.; Bonvin, A.; Boelens, R.; Kaptein, R.
Citation:

Citation: Kalodimos, C.; Biris, N.; Bonvin, A.; Levandoski, M.; Guennuegues, M.; Boelens, R.; Kaptein, R.. "Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes "  Science 305, 386-389 (2004).
PubMed: 15256668

Assembly members:

Assembly members:
Lactose operon repressor, polymer, 62 residues, Formula weight is not available
Binding DNA, polymer, 9 residues, Formula weight is not available
Binding DNA, polymer, 9 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PET-HP62-V52C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Lactose operon repressor: MKPVTLYDVAEYAGVSYQTV SRVVNQASHVSAKTREKVEA AMAELNYIPNRCAQQLAGKQ SL
Binding DNA: CGATAAGAT
Binding DNA: ATCTTATCG

Data typeCount
13C chemical shifts117
1H chemical shifts575
15N chemical shifts69

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1lactose repressor chain A1
2lactose repressor chain B1
3BINDING DNA chain C2
4BINDING DNA chain D3

Entities:

Entity 1, lactose repressor chain A 62 residues - Formula weight is not available

1   METLYSPROVALTHRLEUTYRASPVALALA
2   GLUTYRALAGLYVALSERTYRGLNTHRVAL
3   SERARGVALVALASNGLNALASERHISVAL
4   SERALALYSTHRARGGLULYSVALGLUALA
5   ALAMETALAGLULEUASNTYRILEPROASN
6   ARGCYSALAGLNGLNLEUALAGLYLYSGLN
7   SERLEU

Entity 2, BINDING DNA chain C 9 residues - Formula weight is not available

1   DCDGDADTDADADGDADT

Entity 3, BINDING DNA chain D 9 residues - Formula weight is not available

1   DADTDCDTDTDADTDCDG

Samples:

sample_1: Lactose operon repressor, [U-15N; U-13C], 4 mM; Binding DNA, [U-15N; U-13C], 2 mM; Binding DNA, [U-15N; U-13C], 2 mM; KPI 60 mM; KCL 400 mM; H2O 90%; D2O 10%

sample_cond_1: pH: 5.8 na; temperature: 300 K; ionic strength: 460 mM; pressure: 1 atm

Experiments:

NameSampleSample stateSample conditions
3D 15N-separated NOESYsample_1not availablesample_cond_1
3D 13C-separated NOESYsample_1not availablesample_cond_1
13C-15N double-half noesy filtersample_1not availablesample_cond_1

Software:

XWINNMR v3.0 - collection

NMRPipe v2.1 - processing

NMRVIEW v5.0.3 - data analysis

CNS v1.1 - structure solution, refinement

NMR spectrometers:

  • Bruker DRX 750 MHz

Related Database Links:

BMRB 1066 127 1494 1552 32 4813 5345 661 736 848 849 96
PDB
DBJ BAB20667 BAB33821 BAD00175 BAD20286 BAD20288
EMBL CAA07594 CAA07597 CAA11118 CAA11119 CAA11120
GB AAA24052 AAA56744 AAA56768 AAA57088 AAA57091
REF NP_286086 NP_414879 WP_000718174 WP_000805876 WP_000805884
SP P03023
AlphaFold P03023

Download HSQC peak lists in one of the following formats:
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SPARKY: Backbone or all simulated peaks