BMRB Entry 25102

Name: The NMR structure of the rubredoxin domain of the NO Reductase Flavorubredoxin from Escherichia coli
Published: 2015-07-20

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PDB ID: 2ms3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25102
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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:

The NMR structure of the rubredoxin domain of the NO Reductase Flavorubredoxin from Escherichia coli

Deposition date:

2014-07-22

Original release date:

2015-07-20

Authors:

Turner, David; Silva, Elisio; Lamosa, Pedro; Teixeira, Miguel

Citation:

Citation: Turner, David; Silva, Elisio; Lamosa, Pedro; Teixeira, Miguel. "The NMR structure of the rubredoxin domain of the NO Reductase Flavorubredoxin from Escherichia coli" .

Assembly members:

Assembly members:
rubredoxin_domain_of_the_NO_Reductase_Flavorubredoxin, polymer, 57 residues, 6292.105 Da.
entity_ZN, non-polymer, 65.409 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: PT7-7

Entity Sequences (FASTA):

Entity Sequences (FASTA):
rubredoxin_domain_of_the_NO_Reductase_Flavorubredoxin: GPRMQCSVCQWIYDPAKGEP MQDVAPGTPWSEVPDNFLCP ECSLGKDVFEELASEAK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	54
1H chemical shifts	368

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	rubredoxin domain of the NO Reductase Flavorubredoxin	1
2	ZINC ION	2

Entities:

Entity 1, rubredoxin domain of the NO Reductase Flavorubredoxin 57 residues - 6292.105 Da.

1

GLY

PRO

ARG

MET

GLN

CYS

SER

VAL

CYS

GLN

2

TRP

ILE

TYR

ASP

PRO

ALA

LYS

GLY

GLU

PRO

3

MET

GLN

ASP

VAL

ALA

PRO

GLY

THR

PRO

TRP

4

SER

GLU

VAL

PRO

ASP

ASN

PHE

LEU

CYS

PRO

5

GLU

CYS

SER

LEU

GLY

LYS

ASP

VAL

PHE

GLU

6

GLU

LEU

ALA

SER

GLU

ALA

LYS

Entity 2, ZINC ION - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: rubredoxin domain of the NO Reductase Flavorubredoxin, [U-99% 15N], 1.1 mM; sodium chloride 100 mM; potassium phosphate 10 mM; sodium azide 0.04%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.2 M; pH: 7.7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY v3.111, Goddard - chemical shift calculation, data analysis

DYANA, Guntert, Braun and Wuthrich - refinement, structure solution

NMR spectrometers:

Bruker Avance 800 MHz

PDB	2MS3 4D02
DBJ	BAB36989 BAE76787 BAG78482 BAI26966 BAI31996
EMBL	CAP77145 CAQ33042 CAQ87930 CAQ99627 CAR04219
GB	AAA69220 AAC75752 AAG57817 AAN44224 AAP18050
REF	NP_311593 NP_417190 NP_708517 WP_000029585 WP_000029586
SP	A1AEQ0 A7ZQD9 A8A3I7 B1IUW9 B1LQ28
AlphaFold	A1AEQ0 A7ZQD9 A8A3I7 B1IUW9 B1LQ28