BMRB Entry 17729

Name: Structure of the DNA complex of the C-Terminal domain of Ler
Published: 2011-12-06

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PDB ID: 2lev
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17729
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of the DNA complex of the C-Terminal domain of Ler

Deposition date:

2011-06-23

Original release date:

2011-12-06

Authors:

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

Citation:

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).
PubMed: 22114557

Assembly members:

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:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PHAT2

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	151
15N chemical shifts	59
1H chemical shifts	637

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CT-Ler	1
2	LeeH_A	2
3	LeeH_B	3

Entities:

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

1

SER

HIS

SER

MET

GLY

2

ASN

SER

LYS

GLY

VAL

TYR

ARG

ASN

3

GLU

GLY

GLN

THR

TRP

SER

GLY

VAL

GLY

4

ARG

GLN

PRO

ARG

TRP

LEU

LYS

GLU

ALA

LEU

5

LEU

ASN

GLY

MET

LYS

GLU

ASP

PHE

LEU

6

VAL

LYS

ASP

THR

GLU

Entity 2, LeeH_A 15 residues - 6703.430 Da.

1

DG

DC

DG

DA

DT

DA

DT

DG

2

DA

DT

DA

DG

Entity 3, LeeH_B 15 residues - 6703.430 Da.

1

DC

DT

DA

DT

DC

DA

DT

2

DA

DT

DC

DG

DC

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-1H (13C-ed) NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H (13C-fil) NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H (15N/13C-fil) NOESY	sample_1	isotropic	sample_conditions_1
3D 15N/13C-fil/13c-ed- NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H (13C-fil) TOCSY	sample_2	isotropic	sample_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

PDB	2LEV
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