BMRB Entry 34009

Name: Refined 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli
Published: 2016-08-15

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PDB ID: 5lam
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34009
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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:

Refined 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli

Deposition date:

2016-06-14

Original release date:

2016-08-15

Authors:

Eichmann, C.; Tzitzilonis, C.; Nakamura, T.; Maslennikov, I.; Kwiatkowski, W.; Choe, S.; Lipton, S.; Guntert, P.; Riek, R.

Citation:

Citation: Eichmann, C.; Tzitzilonis, C.; Nakamura, T.; Kwiatkowski, W.; Maslennikov, I.; Choe, S.; Lipton, S.; Riek, R.. "S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein." J. Mol. Biol. 428, 3737-3751 (2016).
PubMed: 27473602

Assembly members:

Assembly members:
entity_1, polymer, 108 residues, 11716.311 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: ALTTISPHDAQELIARGAKL IDIRDADEYLREHIPEADLA PLSVLEQSGLPAKLRHEQII FHCQAGKRTSNNADKLAAIA APAEIFLLEDGIDGWKKAGL PVAVNKSQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	303
15N chemical shifts	110
1H chemical shifts	698

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_1 108 residues - 11716.311 Da.

1

ALA

LEU

THR

ILE

SER

PRO

HIS

ASP

ALA

2

GLN

GLU

LEU

ILE

ALA

ARG

GLY

ALA

LYS

LEU

3

ILE

ASP

ILE

ARG

ASP

ALA

ASP

GLU

TYR

LEU

4

ARG

GLU

HIS

ILE

PRO

GLU

ALA

ASP

LEU

ALA

5

PRO

LEU

SER

VAL

LEU

GLU

GLN

SER

GLY

LEU

6

PRO

ALA

LYS

LEU

ARG

HIS

GLU

GLN

ILE

7

PHE

HIS

CYS

GLN

ALA

GLY

LYS

ARG

THR

SER

8

ASN

ALA

ASP

LYS

LEU

ALA

ILE

ALA

9

ALA

PRO

ALA

GLU

ILE

PHE

LEU

GLU

ASP

10

GLY

ILE

ASP

GLY

TRP

LYS

ALA

GLY

LEU

11

PRO

VAL

ALA

VAL

ASN

LYS

SER

GLN

Samples:

sample_1: Rhodanese domain, [U-99% 13C; U-99% 15N], 1 mM

sample_conditions_1: ionic strength: 0 mM; pH: 7; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
NOESY	sample_1	isotropic	sample_conditions_1
TROSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

OPAL v3.97, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

XEASY, Bartels et al. - chemical shift assignment

NMR spectrometers:

Bruker AvanceIII 700 MHz

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