BMRB Entry 51174

Name: Molecular Dynamics-Assisted Optimization of Protein NMR Relaxation Analysis
Published: 2022-03-04

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51174

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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:

Molecular Dynamics-Assisted Optimization of Protein NMR Relaxation Analysis

Deposition date:

2021-11-10

Original release date:

2022-03-04

Authors:

Anderson, Janet; Hernandez, Griselda; LeMaster, David

Citation:

Citation: Anderson, Janet; Hernandez, Griselda; LeMaster, David. "Molecular Dynamics-Assisted Optimization of Protein NMR Relaxation Analysis" J. Chem. Theory Comput. 18, 2091-2104 (2022).
PubMed: 35245056

Assembly members:

Assembly members:
entity_1, polymer, 76 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pet11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:

heteronucl_NOEs
- heteronucl_NOEs_1
- heteronucl_NOEs_2
heteronucl_T1_relaxation
- heteronucl_T1_relaxation_1
- heteronucl_T1_relaxation_2
heteronucl_T2_relaxation
- heteronucl_T2_relaxation_1
- heteronucl_T2_relaxation_2

Data type	Count
T1 relaxation values	140
T2 relaxation values	140
heteronuclear NOE values	140

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ubiquitin	1

Entities:

Entity 1, ubiquitin 76 residues - Formula weight is not available

1

MET

GLN

ILE

PHE

VAL

LYS

THR

LEU

THR

GLY

2

LYS

THR

ILE

THR

LEU

GLU

VAL

GLU

PRO

SER

3

ASP

THR

ILE

GLU

ASN

VAL

LYS

ALA

LYS

ILE

4

GLN

ASP

LYS

GLU

GLY

ILE

PRO

ASP

GLN

5

GLN

ARG

LEU

ILE

PHE

ALA

GLY

LYS

GLN

LEU

6

GLU

ASP

GLY

ARG

THR

LEU

SER

ASP

TYR

ASN

7

ILE

GLN

LYS

GLU

SER

THR

LEU

HIS

LEU

VAL

8

LEU

ARG

LEU

ARG

GLY

Samples:

sample_1: ubiquitin, [U-15N; U-2H], 0.5 mM; sodium acetate, [U-99% 2H], 25 mM

sample_conditions_1: ionic strength: 16 mM; pH: 5.00; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v3.2.7 - collection

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker Avance 900 MHz