BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 25241

Title: The N-domain of the AAA metalloproteinase Yme1 from Saccharomyces cerevisiae   PubMed: 25576874

Deposition date: 2014-09-22 Original release date: 2015-01-26

Authors: Scharfenberg, Franka; Serek-Heuberger, Justyna; Martin, Joerg; Lupas, Andrei; Coles, Murray

Citation: Scharfenberg, Franka; Serek-Heuberger, Justyna; Coles, Murray; Hartmann, Marcus; Habeck, Michael; Martin, Joerg; Lupas, Andrei; Alva, Vikram. "Structure and Evolution of N-domains in AAA Metalloproteases"  J. Mol. Biol. 427, 910-923 (2015).

Assembly members:
Yme1-N, polymer, 88 residues, 10056.332 Da.

Natural source:   Common Name: Baker's yeast   Taxonomy ID: 559292   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

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

Entity Sequences (FASTA):
Yme1-N: MVAVSHAMLATREQEANKDL TSPDAQAAFYKLLLQSNYPQ YVVSRFETPGIASSPECMEL YMEALQRIGRHSEADAVRQN LEHHHHHH

Data sets:
Data typeCount
13C chemical shifts318
15N chemical shifts56
1H chemical shifts512

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1Yme1-N1

Entities:

Entity 1, Yme1-N 88 residues - 10056.332 Da.

Residues E177-H183 are a non-native affinity tag, residue M96 is a cloning artefact

1   METVALALAVALSERHISALAMETLEUALA
2   THRARGGLUGLNGLUALAASNLYSASPLEU
3   THRSERPROASPALAGLNALAALAPHETYR
4   LYSLEULEULEUGLNSERASNTYRPROGLN
5   TYRVALVALSERARGPHEGLUTHRPROGLY
6   ILEALASERSERPROGLUCYSMETGLULEU
7   TYRMETGLUALALEUGLNARGILEGLYARG
8   HISSERGLUALAASPALAVALARGGLNASN
9   LEUGLUHISHISHISHISHISHIS

Samples:

15N-labelled: Yme1-N, [U-100% 15N], 0.5 mM; TRIS 20 mM; sodium chloride 300 mM; H2O 90%; D2O 10%

13C-15N-labelled: FtsH-N, [U-100% 13C; U-100% 15N], 0.5 mM; TRIS 20 mM; sodium chloride 300 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.340 M; pH: 7.9; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCO13C-15N-labelledisotropicsample_conditions_1
3D C(CO)NH13C-15N-labelledisotropicsample_conditions_1
3D HCCH-TOCSY13C-15N-labelledisotropicsample_conditions_1
3D CCH NOESY13C-15N-labelledisotropicsample_conditions_1
3D CNH NOESY13C-15N-labelledisotropicsample_conditions_1
3D 1H-15N NOESY15N-labelledisotropicsample_conditions_1
3D 1H-13C NOESY13C-15N-labelledisotropicsample_conditions_1
3D HNHA15N-labelledisotropicsample_conditions_1
3D HNHB15N-labelledisotropicsample_conditions_1
3D 3JHBHA(CO)NH13C-15N-labelledisotropicsample_conditions_1
3D NNH NOESY15N-labelledisotropicsample_conditions_1
3D HN(CA)NNH13C-15N-labelledisotropicsample_conditions_1
3D HNCA13C-15N-labelledisotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis

X-PLOR_NIH v2.9.4, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR-SPIRIT v1.1, In house - refinement

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

NCBI NP_015349.1

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts