BMRB Entry 16368

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PDB ID: 2kko
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16368
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:

Solution NMR structure of the homodimeric winged helix-turn-helix DNA-binding domain (fragment 1-100) Mb0332 from Mycobacterium bovis, a possible ArsR-family transcriptional regulator. Northeast Structural Genomics Consortium Target MbR242E.

Deposition date:

2009-06-26

Original release date:

2009-08-06

Authors:

Ramelot, Theresa; Ramelot, John; Wang, D.; Ciccosanti, Colleen; Jiang, Mei; Nair, R.; Rost, Burkhard; Swapna, G.V.T.; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Ramelot, Theresa; Cort, John; Wang, D.; Ciccosanti, Colleen; Jiang, Mei; Nair, R.; Rost, Burkhard; Swapna, G.V.T.; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael. "Solution NMR structure of the homodimeric winged helix-turn-helix DNA-binding domain (fragment 1-100) Mb0332 from Mycobacterium bovis, a possible ArsR-family transcriptional regulator. Northeast Structural Genomics Consortium Target MbR242E." .

Assembly members:

Assembly members:
Mb0332, polymer, 109 residues, 11700 Da.

Natural source:

Natural source: Common Name: Mycobacterium bovis Taxonomy ID: 1765 Superkingdom: Bacteria Kingdom: not available Genus/species: Mycobacterium bovis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21-23C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Mb0332: XMAGQSDRKAALLDQVARVG KALANGRRLQILDLLAQGER AVEAIATATGMNLTTASANL QALKSGGLVEARREGTRQYY RIAGEDVARLFALVQVVADE HLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	431
15N chemical shifts	116
1H chemical shifts	720

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Mb0332, chain A	1
2	Mb0332, chain B	1

Entities:

Entity 1, Mb0332, chain A 109 residues - 11700 Da.

8 non-native residues at C-terminus (LEHHHHHH)

1

ACE

MET

ALA

GLY

GLN

SER

ASP

ARG

LYS

ALA

2

ALA

LEU

ASP

GLN

VAL

ALA

ARG

VAL

GLY

3

LYS

ALA

LEU

ALA

ASN

GLY

ARG

LEU

GLN

4

ILE

LEU

ASP

LEU

ALA

GLN

GLY

GLU

ARG

5

ALA

VAL

GLU

ALA

ILE

ALA

THR

ALA

THR

GLY

6

MET

ASN

LEU

THR

ALA

SER

ALA

ASN

LEU

7

GLN

ALA

LEU

LYS

SER

GLY

LEU

VAL

GLU

8

ALA

ARG

GLU

GLY

THR

ARG

GLN

TYR

9

ARG

ILE

ALA

GLY

GLU

ASP

VAL

ALA

ARG

LEU

10

PHE

ALA

LEU

VAL

GLN

VAL

ALA

ASP

GLU

11

HIS

LEU

GLU

HIS

Samples:

NC_sample: MES 20 ± 2.5 mM; sodium chloride 200 ± 10 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %; protein, [U-100% 13C; U-100% 15N], 1.1 ± 0.05 mM; DSS 50 ± 2.5 uM; H2O 95%; D2O 5%

NC5_sample: MES 20 ± 2.5 mM; sodium chloride 200 ± 2.5 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %; protein, [U-5% 13C; U-100% 15N], 0.8 ± 0.1 mM; DSS 50 ± 2.5 uM; H2O 95%; D2O 5%

NC50_sample: MES 20 ± 2.5 mM; sodium chloride 200 ± 2.5 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %; protein, [U-100% 13C; U-100% 15N], 0.5 ± 0.05 mM; DSS 50 ± 2.5 uM; protein .5 ± 0.05 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC_sample	isotropic	sample_conditions_1
3D 1H-15N NOESY	NC_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY	NC_sample	isotropic	sample_conditions_1
3D HNCO	NC_sample	isotropic	sample_conditions_1
3D HNCA	NC_sample	isotropic	sample_conditions_1
3D CBCA(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HNCACB	NC_sample	isotropic	sample_conditions_1
3D C(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HBHA(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HCCH-TOCSY	NC_sample	isotropic	sample_conditions_1
3D HCCH-COSY	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC arom	NC5_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY arom	NC_sample	isotropic	sample_conditions_1
3D CN filt 1H-13C NOESY	NC50_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC50_sample	isotropic	sample_conditions_1
3D HNCOCA	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC aliph	NC5_sample	isotropic	sample_conditions_1
2D 1H-15N HSQC	NC5_sample	isotropic	sample_conditions_1

Software:

NMRPipe v2008, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMR v6.1C, Varian - collection

TOPSPIN v2.1.3, Bruker Biospin - collection

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - data analysis

X-PLOR NIH v2.20, Schwieters, Kuszewski, Tjandra and Clore - structure solution

SPARKY v3.113, Goddard - data analysis

PSVS v1.3, Bhattacharya and Montelione - structure validation

AutoAssign v2.3.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

PDBStat v5.1, (PDBStat) R. Tejero, G.T. Montelione - data analysis

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Varian INOVA 600 MHz
Bruker AvanceIII 850 MHz
Varian INOVA 750 MHz

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