BMRB Entry 15487

Name: Segmental Isotope Labeling of Npl3p
Published: 2008-06-26

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PDB ID: 2jvr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15487
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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:

Segmental Isotope Labeling of Npl3p

Deposition date:

2007-09-25

Original release date:

2008-06-26

Authors:

Skrisovska, Lenka; Allain, Frederic

Citation:

Citation: Skrisovska, Lenka; Allain, Frederic. "Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: application to the RRMs of Npl3p and hnRNP L" J. Mol. Biol. 375, 151-164 (2008).
PubMed: 17936301

Assembly members:

Assembly members:
Npl3p_RRM2, polymer, 111 residues, 12545 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a+

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Npl3p_RRM2: MGSSHHHHHHSSGLVPRGSH MSKLPAKRYRITMKNLPEGC SWQDLKDLARENSLETTFSS VNTRDFDGTGALEFPSEEIL VEALERLNNIEFRGSVITVE RDDNPPPIRRS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	230
15N chemical shifts	82
1H chemical shifts	501

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Npl3p RRM2	1

Entities:

Entity 1, Npl3p RRM2 111 residues - 12545 Da.

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

SER

LYS

LEU

PRO

ALA

LYS

ARG

TYR

ARG

4

ILE

THR

MET

LYS

ASN

LEU

PRO

GLU

GLY

CYS

5

SER

TRP

GLN

ASP

LEU

LYS

ASP

LEU

ALA

ARG

6

GLU

ASN

SER

LEU

GLU

THR

PHE

SER

7

VAL

ASN

THR

ARG

ASP

PHE

ASP

GLY

THR

GLY

8

ALA

LEU

GLU

PHE

PRO

SER

GLU

ILE

LEU

9

VAL

GLU

ALA

LEU

GLU

ARG

LEU

ASN

ILE

10

GLU

PHE

ARG

GLY

SER

VAL

ILE

THR

VAL

GLU

11

ARG

ASP

ASN

PRO

ILE

ARG

12

SER

Samples:

sample_1: Npl3p RRM2, [U-13C; U-15N], 1 mM; H2O 90%; D2O 10%

sample_2: Npl3p RRM2, [U-13C; U-15N], 1 mM; D2O 10%

sample_3: Npl3p RRM2, [U-15N], 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.2 M; pH: 7; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

ATHNOS-CANDID, T. Herrmann 2005 - automated NOE assignment, automated peak picking, structure calculation

AMBER v7.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Koll - refinement

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DRX 600 MHz
Bruker Avance 900 MHz

PDB	2JVR 2OSR
DBJ	GAA22648
EMBL	CAA46817 CAA50291 CAY78932
GB	AAA34818 AAB64865 AHY75384 AJP38110 AJU58232
REF	NP_010720
SP	Q01560
TPG	DAA12270
AlphaFold	Q01560