BMRB Entry 30611

Name: NMR solution structure of YfiD
Published: 2019-07-05

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PDB ID: 6owr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30611
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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:

NMR solution structure of YfiD

Deposition date:

2019-05-10

Original release date:

2019-07-05

Authors:

Bowman, S.; Drennan, C.

Citation:

Citation: Bowman, S.; Backman, L.; Bjork, R.; Andorfer, M.; Yori, S.; Caruso, A.; Stultz, C.; Drennan, C.. "Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme." J. Biol. Inorg. Chem. 24, 817-829 (2019).
PubMed: 31250200

Assembly members:

Assembly members:
entity_1, polymer, 127 residues, 14286.153 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: p-CAL-n-EK

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MITGIQITKAANDDLLNSFW LLDSEKGEARCIVAKAGFAE DEVVAVSKLGDIEYREVPVE VKPEVRVEGGQHLNVNVLRR ETLEDAVKHPEKYPQLTIRV SGYAVRFNSLTPEQQRDVIA RTFTESL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	76
15N chemical shifts	57
1H chemical shifts	349

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 127 residues - 14286.153 Da.

1

MET

ILE

THR

GLY

ILE

GLN

ILE

THR

LYS

ALA

2

ALA

ASN

ASP

LEU

ASN

SER

PHE

TRP

3

LEU

ASP

SER

GLU

LYS

GLY

GLU

ALA

ARG

4

CYS

ILE

VAL

ALA

LYS

ALA

GLY

PHE

ALA

GLU

5

ASP

GLU

VAL

ALA

VAL

SER

LYS

LEU

GLY

6

ASP

ILE

GLU

TYR

ARG

GLU

VAL

PRO

VAL

GLU

7

VAL

LYS

PRO

GLU

VAL

ARG

VAL

GLU

GLY

8

GLN

HIS

LEU

ASN

VAL

ASN

VAL

LEU

ARG

9

GLU

THR

LEU

GLU

ASP

ALA

VAL

LYS

HIS

PRO

10

GLU

LYS

TYR

PRO

GLN

LEU

THR

ILE

ARG

VAL

11

SER

GLY

TYR

ALA

VAL

ARG

PHE

ASN

SER

LEU

12

THR

PRO

GLU

GLN

ARG

ASP

VAL

ILE

ALA

13

ARG

THR

PHE

THR

GLU

SER

LEU

Samples:

sample_1: YfiD, [U-15N], 0.7 mM; HEPES 18 mM; ammonium sulfate 2.7 mM; D2O 10 % v/v

sample_2: YfiD, [U-100% 13C; U-100% 15N], 1.3 mM; HEPES 18 mM; ammonium sulfate 2.7 mM; D2O 10 % v/v

sample_conditions_1: ionic strength: 2.7 mM; pH: 7.2; pressure: 760 mmHg; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1

Software:

VNMR, Varian - collection

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

Sparky, Goddard - chemical shift assignment, peak picking, structure calculation

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Varian INOVA 800 MHz
FBML CMR 600 E 600 MHz

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