BMRB Entry 16843

Name: Seeing the Invisible: Structures of Excited Protein States by Relaxation Dispersion NMR
Published: 2012-08-03

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PDB ID: 2k3b
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16843
MolProbity Validation Chart

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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:

Seeing the Invisible: Structures of Excited Protein States by Relaxation Dispersion NMR

Deposition date:

2010-04-06

Original release date:

2012-08-03

Authors:

Vallurupalli, Pramodh; Hansen, Flemming; Kay, Lewis

Citation:

Citation: Sanchez-Medina, Celia; Sekhar, Ashok; Vallurupalli, Pramodh; Cerminara, Michele; Munoz, Victor; Kay, Lewis. "Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMR." J. Am. Chem. Soc. ., .-. (2014).
PubMed: 24805164

Assembly members:

Assembly members:
Abp1p, polymer, 62 residues, Formula weight is not available
Ark1p, polymer, 17 residues, Formula weight is not available

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: pET32b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Abp1p: GAMAPWATAEYDYDAAEDNE LTFVENDKIINIEFVDDDWW LGELEKDGSKGLFPSNYVSL GN
Ark1p: KKTKPTPPPKPSHLKPK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	99
15N chemical shifts	57
1H chemical shifts	56

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Abp1p	1
2	Ark1p	2

Entities:

Entity 1, Abp1p 62 residues - Formula weight is not available

Starting Residues GAM are not numbered and not used.

1

GLY

ALA

MET

ALA

PRO

TRP

ALA

THR

ALA

GLU

2

TYR

ASP

TYR

ASP

ALA

GLU

ASP

ASN

GLU

3

LEU

THR

PHE

VAL

GLU

ASN

ASP

LYS

ILE

4

ASN

ILE

GLU

PHE

VAL

ASP

TRP

5

LEU

GLY

GLU

LEU

GLU

LYS

ASP

GLY

SER

LYS

6

GLY

LEU

PHE

PRO

SER

ASN

TYR

VAL

SER

LEU

7

GLY

ASN

Entity 2, Ark1p 17 residues - Formula weight is not available

1

LYS

THR

LYS

PRO

THR

PRO

LYS

2

PRO

SER

HIS

LEU

LYS

PRO

LYS

Samples:

sample_1: Abp1p, [U-90% 2H; U-100% 15N], 1.5 mM; Ark1p, [U-90% 2H; U-100% 15N], 0.105 mM; Sodium Phosphate 50 mM; NaCl 100 mM; EDTA 1 mM; NaN3 1 mM

sample_2: Abp1p, [U-90% 2H; U-100% 15N], 1.5 mM; Ark1p 0.105 mM; Sodium Phosphate 50 mM; NaCl 100 mM; EDTA 1 mM; NaN3 1 mM

sample_3: Abp1p, [U-90% 2H; U-100% 15N; 13CO labeled], 1.5 mM; Ark1p 0.105 mM; Sodium Phosphate 50 mM; NaCl 100 mM; EDTA 1 mM; NaN3 1 mM

sample_4: Abp1p, [U-90% 2H; U-100% 15N; 13Ca labeled], 1.5 mM; Ark1p 0.105 mM; Sodium Phosphate 50 mM; NaCl 100 mM; EDTA 1 mM; NaN3 1 mM

sample_conditions_1: ionic strength: 0.150 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
15N CT-CW,TROSY,anti-TROSY CPMG	sample_1	anisotropic	sample_conditions_1
15N CT-CW,TROSY,anti-TROSY CPMG	sample_2	anisotropic	sample_conditions_1
13CO CT-inphase,TROSY,anti-TROSY CPMG	sample_3	anisotropic	sample_conditions_1
13CA CT-CW,TROSY,anti-TROSY CPMG	sample_4	anisotropic	sample_conditions_1
15N CT-CW CPMG	sample_2	isotropic	sample_conditions_1
13 CO CT CPMG	sample_3	isotropic	sample_conditions_1
13 CA CT-CW CPMG	sample_4	isotropic	sample_conditions_1
1H CT-CW CPMG	sample_2	isotropic	sample_conditions_1

Software:

X-PLOR NIH v2.19, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 800 MHz
Varian INOVA 600 MHz

BMRB	18054 18055 18056 18057 18058 18059 18060 18061 18062 18063 18064 18065 18066 18067 18068 18069 18070 18071 18072 18073 18074 18075 18076 18077 18078 25354 26519 17223 18055 18067
PDB	1JO8 2K3B 2RPN 2RPN
DBJ	GAA21988 GAA26063
EMBL	CAA36075 CAA42253 CAY78291 CAA95882
GB	AHN96147 AHV79349 AHY79755 AJP37506 AJQ31991 AHY77072 EDN62778 EDV12290 EEU04773 EGA56977
PRF	1603360A
REF	NP_010012 NP_014378
SP	P15891 P53974
TPG	DAA07557 DAA10525
AlphaFold	P15891 P53974