BMRB Entry 52376

Name: Chemical shifts of folding intermediate N'
Published: 2024-04-02

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52376

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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:

Chemical shifts of folding intermediate N'

Deposition date:

2024-03-28

Original release date:

2024-04-02

Authors:

Adhada, Sri Teja; Sarma, Siddhartha

Citation:

Citation: Adhada, Sri Teja; Sarma, Siddhartha. "Slow conformational exchange between partially folded and near native states of Ubiquitin suggest a multi-state folding model" .

Assembly members:

Assembly members:
entity_1, polymer, 77 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Japanese rice Taxonomy ID: 39947 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Oryza sativa

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21a(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MMQIFVKTLTGKTITLEVES SDTIDNVKAKIQDKEGIPPD QQRLIFAGKQLEDGRTLADY NIQKESTLHLVLRLRGG'

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	324
15N chemical shifts	74
1H chemical shifts	74

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ubiquitin folding intermediate	1

Entities:

Entity 1, Ubiquitin folding intermediate 77 residues - Formula weight is not available

1

MET

GLN

ILE

PHE

VAL

LYS

THR

LEU

THR

2

GLY

LYS

THR

ILE

THR

LEU

GLU

VAL

GLU

SER

3

SER

ASP

THR

ILE

ASP

ASN

VAL

LYS

ALA

LYS

4

ILE

GLN

ASP

LYS

GLU

GLY

ILE

PRO

ASP

5

GLN

ARG

LEU

ILE

PHE

ALA

GLY

LYS

GLN

6

LEU

GLU

ASP

GLY

ARG

THR

LEU

ALA

ASP

TYR

7

ASN

ILE

GLN

LYS

GLU

SER

THR

LEU

HIS

LEU

8

VAL

LEU

ARG

LEU

ARG

GLY

Samples:

sample_1: Ubiquitin from Rice (Oryza sativa) 1 ± 0.1 mM

sample_2: Ubiquitin from Rice (Oryza sativa), [U-15N], 1 ± 0.1 mM

sample_3: Ubiquitin from Rice (Oryza sativa), [U-13C; U-15N], 1 ± 0.1 mM

sample_conditions_1: ionic strength: 20 mM; pH: 2; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_3	isotropic	sample_conditions_1
3D HN(CA)CO	sample_3	isotropic	sample_conditions_1
3D C(CO)NH	sample_3	isotropic	sample_conditions_1

Software:

CcpNMR v2.5.2 - chemical shift assignment, peak picking

NMRPipe v10.9 - data analysis, processing

VNMRj v4.2 - collection

TOPSPIN v4.0.9 - collection

NMR spectrometers:

Bruker Avance 700 MHz
Agilent DirectDrive 600 MHz

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