BMRB Entry 25702

Name: Structures of the reduced and oxidized state of the mutant D24A of yeast thioredoxin 1: insight into the mechanism for the closing of the water cavity
Published: 2015-10-26

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PDB ID: 2n5a
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25702
MolProbity Validation Chart

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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:

Structures of the reduced and oxidized state of the mutant D24A of yeast thioredoxin 1: insight into the mechanism for the closing of the water cavity

Deposition date:

2015-07-13

Original release date:

2015-10-26

Authors:

Iqbal, Anwar; Moraes, Adolfo; Valente, Ana Paula; Almeida, Fabio

Citation:

Citation: Iqbal, Anwar; Moraes, Adolfo; Valente, Ana Paula; Almeida, Fabio. "Structures of the reduced and oxidized state of the mutant D24A of yeast thioredoxin 1: insights into the mechanism for the closing of the water cavity" J. Biomol. NMR 63, 417-423 (2015).
PubMed: 26482062

Assembly members:

Assembly members:
Yeast_Thioredoxin_1_redcuced, polymer, 103 residues, 11201.019 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: not available Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PET17B

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Yeast_Thioredoxin_1_redcuced: MVTQFKTASEFDSAIAQDKL VVVAFYATWCGPCKMIAPMI EKFSEQYPQADFYKLDVDEL GDVAQKNEVSAMPTLLLFKN GKEVAKVVGANPAAIKQAIA ANA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	380
15N chemical shifts	102
1H chemical shifts	599

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	reduced form of thioredoxin 1 from Sacharomyces cerevisiae	1

Entities:

Entity 1, reduced form of thioredoxin 1 from Sacharomyces cerevisiae 103 residues - 11201.019 Da.

1

MET

VAL

THR

GLN

PHE

LYS

THR

ALA

SER

GLU

2

PHE

ASP

SER

ALA

ILE

ALA

GLN

ASP

LYS

LEU

3

VAL

ALA

PHE

TYR

ALA

THR

TRP

CYS

4

GLY

PRO

CYS

LYS

MET

ILE

ALA

PRO

MET

ILE

5

GLU

LYS

PHE

SER

GLU

GLN

TYR

PRO

GLN

ALA

6

ASP

PHE

TYR

LYS

LEU

ASP

VAL

ASP

GLU

LEU

7

GLY

ASP

VAL

ALA

GLN

LYS

ASN

GLU

VAL

SER

8

ALA

MET

PRO

THR

LEU

PHE

LYS

ASN

9

GLY

LYS

GLU

VAL

ALA

LYS

VAL

GLY

ALA

10

ASN

PRO

ALA

ILE

LYS

GLN

ALA

ILE

ALA

11

ALA

ASN

ALA

Samples:

D24A_reduced: yTrx1D24A reduced, [U-100% 13C; U-100% 15N], 850 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.02 M; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	D24A_reduced	isotropic	sample_conditions_1
2D 1H-13C HSQC	D24A_reduced	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	D24A_reduced	isotropic	sample_conditions_1
3D CBCA(CO)NH	D24A_reduced	isotropic	sample_conditions_1
3D HNCO	D24A_reduced	isotropic	sample_conditions_1
3D HNCACB	D24A_reduced	isotropic	sample_conditions_1
3D HCCH-TOCSY	D24A_reduced	isotropic	sample_conditions_1
3D HCCH-COSY	D24A_reduced	isotropic	sample_conditions_1
3D HBHA(CO)NH	D24A_reduced	isotropic	sample_conditions_1
3D 1H-15N NOESY	D24A_reduced	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	D24A_reduced	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	D24A_reduced	isotropic	sample_conditions_1

Software:

ARIA varia2.3, Brunger, Adams, Clore, Gros, Nilges and Read, Linge, O'Donoghue and Nilges - refinement, structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz

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