BMRB Entry 25241

Name: The N-domain of the AAA metalloproteinase Yme1 from Saccharomyces cerevisiae
Published: 2015-01-26

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PDB ID: 2mv3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25241
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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 N-domain of the AAA metalloproteinase Yme1 from Saccharomyces cerevisiae

Deposition date:

2014-09-22

Original release date:

2015-01-26

Authors:

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

Citation:

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).
PubMed: 25576874

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET30a

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	318
15N chemical shifts	56
1H chemical shifts	512

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Yme1-N	1

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

MET

VAL

ALA

VAL

SER

HIS

ALA

MET

LEU

ALA

2

THR

ARG

GLU

GLN

GLU

ALA

ASN

LYS

ASP

LEU

3

THR

SER

PRO

ASP

ALA

GLN

ALA

PHE

TYR

4

LYS

LEU

GLN

SER

ASN

TYR

PRO

GLN

5

TYR

VAL

SER

ARG

PHE

GLU

THR

PRO

GLY

6

ILE

ALA

SER

PRO

GLU

CYS

MET

GLU

LEU

7

TYR

MET

GLU

ALA

LEU

GLN

ARG

ILE

GLY

ARG

8

HIS

SER

GLU

ALA

ASP

ALA

VAL

ARG

GLN

ASN

9

LEU

GLU

HIS

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:

Name	Sample	Sample state	Sample conditions
3D HNCO	13C-15N-labelled	isotropic	sample_conditions_1
3D C(CO)NH	13C-15N-labelled	isotropic	sample_conditions_1
3D HCCH-TOCSY	13C-15N-labelled	isotropic	sample_conditions_1
3D CCH NOESY	13C-15N-labelled	isotropic	sample_conditions_1
3D CNH NOESY	13C-15N-labelled	isotropic	sample_conditions_1
3D 1H-15N NOESY	15N-labelled	isotropic	sample_conditions_1
3D 1H-13C NOESY	13C-15N-labelled	isotropic	sample_conditions_1
3D HNHA	15N-labelled	isotropic	sample_conditions_1
3D HNHB	15N-labelled	isotropic	sample_conditions_1
3D 3JHBHA(CO)NH	13C-15N-labelled	isotropic	sample_conditions_1
3D NNH NOESY	15N-labelled	isotropic	sample_conditions_1
3D HN(CA)NNH	13C-15N-labelled	isotropic	sample_conditions_1
3D HNCA	13C-15N-labelled	isotropic	sample_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