BMRB Entry 18496

Name: Solution NMR Structure of YdbC:dT19G1 complex. Northeast Structural Genomics Consortium (NESG) Target KR150
Published: 2012-07-02

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PDB ID: 2ltt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18496
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR Structure of YdbC:dT19G1 complex. Northeast Structural Genomics Consortium (NESG) Target KR150

Deposition date:

2012-05-31

Original release date:

2012-07-02

Authors:

Rossi, Paolo; Barbieri, Christopher; Aramini, James; Bini, Elisabetta; Lee, Hsiau-Wei; Janjua, Haleema; Ciccosanti, Colleen; Wang, Huang; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano

Citation:

Citation: Rossi, Paolo; Barbieri, Christopher; Aramini, James; Bini, Elisabetta; Acton, Thomas; Xiao, Rong; Montelione, Gaetano. "Solution NMR Structure of YdbC:dT19G1 complex. Northeast Structural Genomics Consortium (NESG) Target KR150" To be published ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 74 residues, 8659.957 Da.
DNA_(5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')_, polymer, 14 residues, 4213.782 Da.

Natural source:

Natural source: Common Name: Lactococcus Lactis Taxonomy ID: 1358 Superkingdom: Bacteria Kingdom: not available Genus/species: Lactococcus Lactis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21_NESG

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MADKLKFEIIEELIVLSENA KGWRKELNRVSWNDAEPKYD IRTWSPDHEKMGKGITLSEE EFGVLLKELGNKLE
DNA_(5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')_: TTTTTTTTTTTTTT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	330
15N chemical shifts	70
1H chemical shifts	655

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	KR150_1	1
2	KR150_2	1
3	DNA (5'-D(TPTPTPTPTPTPTPTPTPTPTPTPTPT)-3')	2

Entities:

Entity 1, KR150_1 74 residues - 8659.957 Da.

1

MET

ALA

ASP

LYS

LEU

LYS

PHE

GLU

ILE

2

GLU

LEU

ILE

VAL

LEU

SER

GLU

ASN

ALA

3

LYS

GLY

TRP

ARG

LYS

GLU

LEU

ASN

ARG

VAL

4

SER

TRP

ASN

ASP

ALA

GLU

PRO

LYS

TYR

ASP

5

ILE

ARG

THR

TRP

SER

PRO

ASP

HIS

GLU

LYS

6

MET

GLY

LYS

GLY

ILE

THR

LEU

SER

GLU

7

GLU

PHE

GLY

VAL

LEU

LYS

GLU

LEU

GLY

8

ASN

LYS

LEU

GLU

Entity 2, DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') 14 residues - 4213.782 Da.

1

DT

2

DT

Samples:

sample_1: KR150.020, [U-100% 13C; U-100% 15N], 0.6 mM; NaN3 0.02%; DTT 10 mM; NaCL 100 mM; D2O 10%; DSS 50 uM; TRIS-HCl 10 mM; DNA chain 0.3 mM; H2O 90%

sample_conditions_1: pH: 7.5; 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	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D-13C,15N X-filt-13C,15N-edited NOESY	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
1H-15N Hetnoe	sample_1	isotropic	sample_conditions_1
1D T1	sample_1	isotropic	sample_conditions_1
1D T2(cpmg)	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinemen,structure solution,geometry optimization

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement,geometry optimization,structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN, Bruker Biospin - collection

VNMRJ, Varian - collection

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

SPARKY, Goddard - data analysis

TALOS+, Shen, Cornilescu, Delaglio and Bax - geometry optimization

PALES, PALES (Zweckstetter, Bax) - geometry optimization

PSVS, Bhattacharya, Montelione - structure validation

HADDOCK, Bonvin A. M. J. J. - refinemen,structure solution,geometry optimization

NMR spectrometers:

Bruker Avance 800 MHz

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