BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17729

Title: Structure of the DNA complex of the C-Terminal domain of Ler   PubMed: 22114557

Authors: Cordeiro, Tiago; Schimdt, Holger; Grisienger, Christian; Pons, Miquel; Cordeiro, Tiago

Citation: Cordeiro, Tiago; Schimdt, Holger; Madrid, Cristina; Juarez, Antonio; Bernado, Pau; Grisienger, Christian; Garcia, Jesus; Pons, Miquel. "Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler"  PLoS Pathog. 7, e1002380-. (2011).

Assembly members:
CT-Ler, polymer, 57 residues, 6703.430 Da.
LeeH_A, polymer, 15 residues, 6703.430 Da.
LeeH_B, polymer, 15 residues, 6703.430 Da.

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
CT-Ler: SHHHHHHSMGNSSKGVYYRN EEGQTWSGVGRQPRWLKEAL LNGMKKEDFLVKDTEEE
LeeH_A: GCGATAATTGATAGG
LeeH_B: CCTATCAATTATCGC

Data sets:
Data typeCount
13C chemical shifts151
15N chemical shifts59
1H chemical shifts637

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1CT-Ler1
2LeeH_A2
3LeeH_B3

Entities:

Entity 1, CT-Ler 57 residues - 6703.430 Da.

1   SERHISHISHISHISHISHISSERMETGLY
2   ASNSERSERLYSGLYVALTYRTYRARGASN
3   GLUGLUGLYGLNTHRTRPSERGLYVALGLY
4   ARGGLNPROARGTRPLEULYSGLUALALEU
5   LEUASNGLYMETLYSLYSGLUASPPHELEU
6   VALLYSASPTHRGLUGLUGLU

Entity 2, LeeH_A 15 residues - 6703.430 Da.

1   DGDCDGDADTDADADTDTDG
2   DADTDADGDG

Entity 3, LeeH_B 15 residues - 6703.430 Da.

1   DCDCDTDADTDCDADADTDT
2   DADTDCDGDC

Samples:

sample_1: CT-Ler, [U-100% 13C; U-100% 15N], 1 mM; LeeH_A 2 mM; LeeH_B 2 mM; sodium phosphate 20 mM; sodium chloride 20 mM; sodium azide 0.01 %(w/v); EDTA 0.2 mM; H2O 90%; D2O 10%

sample_2: CT-Ler, [U-100% 13C; U-100% 15N], 1 mM; LeeH_A 2 mM; LeeH_B 2 mM; sodium phosphate 20 mM; sodium chloride 150 mM; sodium azide 0.01 %(w/v); EDTA 0.2 mM; D2O 100%

sample_3: CT-Ler, [U-10% 13C; U-100% 15N], 1 mM; LeeH_A 2 mM; LeeH_B 2 mM; sodium phosphate 20 mM; sodium chloride 150 mM; sodium azide 0.01 % (w/v); EDTA 0.2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 150 mM; pH: 5.7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
2D 1H-1H (13C-ed) NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H (13C-fil) NOESYsample_2isotropicsample_conditions_1
2D 1H-1H (15N/13C-fil) NOESYsample_1isotropicsample_conditions_1
3D 15N/13C-fil/13c-ed- NOESYsample_1isotropicsample_conditions_1
2D 1H-1H (13C-fil) TOCSYsample_2isotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Zhengrong and Bax - Processing

TOPSPIN, Bruker Biospin - NMR spectra acquisition

CYANA, Guntert, Mumenthaler and Wuthrich - Structure Calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - Energy water refinement

CARA, Keller and Wuthrich - Chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - Prediction of Protein Phi and Psi Angles Using a Chemical Shift Database

CRYSOL, Svergun D.I., Barberato C. and Koch M.H.J. - Fitting to experimental scattering curves

HADDOCK, Alexandre Bonvin - Data-driven docking using CNS as structure calculation engine

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - molecular dynamics refinement

Procheck, Laskowski and MacArthur - Quality assessment

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB
DBJ BAB38011 BAI28393 BAI32361 BAI37557 BAT37610
EMBL CAC81843 CAG17510 CAI43893 CAR47961 CAS11516
GB AAC31533 AAC38364 AAG58852 AAK26696 AAL57523
REF NP_312615 WP_001055727 WP_001055728 WP_001310359 WP_001339878