BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 34009

Title: Refined 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli   PubMed: 27473602

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: 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).

Assembly members:
entity_1, polymer, 108 residues, 11716.311 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

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

Data sets:
Data typeCount
13C chemical shifts303
15N chemical shifts110
1H chemical shifts698

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 108 residues - 11716.311 Da.

1   ALALEUTHRTHRILESERPROHISASPALA
2   GLNGLULEUILEALAARGGLYALALYSLEU
3   ILEASPILEARGASPALAASPGLUTYRLEU
4   ARGGLUHISILEPROGLUALAASPLEUALA
5   PROLEUSERVALLEUGLUGLNSERGLYLEU
6   PROALALYSLEUARGHISGLUGLNILEILE
7   PHEHISCYSGLNALAGLYLYSARGTHRSER
8   ASNASNALAASPLYSLEUALAALAILEALA
9   ALAPROALAGLUILEPHELEULEUGLUASP
10   GLYILEASPGLYTRPLYSLYSALAGLYLEU
11   PROVALALAVALASNLYSSERGLN

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:

NameSampleSample stateSample conditions
NOESYsample_1isotropicsample_conditions_1
TROSYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_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 simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts