BMRB Entry 34449

Name: Solution Structure of the DNA-binding TubR fragment from Clostridium Botulinum
Published: 2020-11-12

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PDB ID: 6tey
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34449
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of the DNA-binding TubR fragment from Clostridium Botulinum

Deposition date:

2019-11-12

Original release date:

2020-11-12

Authors:

Valverde, P.; Canada, F.; Jimenez-Barbero, J.; Oliva, M.

Citation:

Citation: Valverde, P.; Canada, F.; Jimenez-Barbero, J.; Oliva, M.. "Structure of TubR protein fragment from Clostridium Botulinum's phage c-st" .

Assembly members:

Assembly members:
entity_1, polymer, 81 residues, 9434.286 Da.

Natural source:

Natural source: Common Name: Clostridium phage c-st Taxonomy ID: 12336 Superkingdom: Viruses Kingdom: not available Genus/species: not available Clostridium phage c-st

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MAVNKNEYKILIMLKENQCT TELKSFTYTKLCNISKLSMS TVRRSIKKFLELQYVKEGCK QGISKTFYITPNGIEKLKSI M

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	381
15N chemical shifts	77
1H chemical shifts	613

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 81 residues - 9434.286 Da.

1

MET

ALA

VAL

ASN

LYS

ASN

GLU

TYR

LYS

ILE

2

LEU

ILE

MET

LEU

LYS

GLU

ASN

GLN

CYS

THR

3

THR

GLU

LEU

LYS

SER

PHE

THR

TYR

THR

LYS

4

LEU

CYS

ASN

ILE

SER

LYS

LEU

SER

MET

SER

5

THR

VAL

ARG

SER

ILE

LYS

PHE

LEU

6

GLU

LEU

GLN

TYR

VAL

LYS

GLU

GLY

CYS

LYS

7

GLN

GLY

ILE

SER

LYS

THR

PHE

TYR

ILE

THR

8

PRO

ASN

GLY

ILE

GLU

LYS

LEU

LYS

SER

ILE

9

MET

Samples:

sample_1: TubR, [U-15N], 225 ± 1 uM; potassium phosphate 25 ± 0.1 mM; potassium chloride 50 ± 0.1 mM; DTT, D-10, 2 ± 0.1 mM

sample_conditions_1: ionic strength: 80.13 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

MolProbity, Richardson - geometry optimization, refinement

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker AVANCE 600 MHz
Bruker AVANCE 600 MHz

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