BMRB Entry 26506

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26506

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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:

Analysis of 15N-1H NMR Relaxation in Proteins by a Combined Experimental and Molecular Dynamics Simulation Approach: Picosecond-Nanosecond Dynamics of the Rho GTPase Binding Domain of Plexin-B1 in the Dimeric State Indicates Allosteric Pathways

Deposition date:

2015-01-29

Original release date:

2015-02-09

Authors:

Zerbetto, Mirco; Anderson, Ross; Bouguet-Bonnet, Sabine; Rech, Mariano; Zhang, Liqun; Meirovitch, Eva; Polimeno, Anonino; Buck, Matthias

Citation:

Citation: Zerbetto, Mirco; Anderson, Ross; Bouguet-Bonnet, Sabine; Rech, Mariano; Zhang, Liqun; Meirovitch, Eva; Polimeno, Anonino; Buck, Matthias. "Analysis of 15N-1H NMR Relaxation in Proteins by a Combined Experimental and Molecular Dynamics Simulation Approach: Picosecond-Nanosecond Dynamics of the Rho GTPase Binding Domain of Plexin-B1 in the Dimeric State Indicates Allosteric Pathways" J. Phys. Chem. B 117, 174-184 (2012).
PubMed: 23214953

Assembly members:

Assembly members:
RBD, polymer, 122 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):
RBD: KKDVEYRPLTLNALLAVGPG AGEAQGVPVKVLDCDTISQA KEKMLDQLYKGVPLTQRPDP RTLDVEWRSGVAGHLILSDE DVTSEVQGLFRRLNTLQHYK VPDGATVALVPCLTKHVLRE NK

Data sets:

heteronucl_NOEs
- heteronuclear_noe_list_1
- heteronuclear_noe_list_2
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
- heteronuclear_T1_list_2
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
- heteronuclear_T2_list_2
order_parameters
- order_parameter_list_1

Data type	Count
T1 relaxation values	194
T2 relaxation values	194
heteronuclear NOE values	194
order parameters	68

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Rho-GTPase Binding Domain	1

Entities:

Entity 1, Rho-GTPase Binding Domain 122 residues - Formula weight is not available

1

LYS

ASP

VAL

GLU

TYR

ARG

PRO

LEU

THR

2

LEU

ASN

ALA

LEU

ALA

VAL

GLY

PRO

GLY

3

ALA

GLY

GLU

ALA

GLN

GLY

VAL

PRO

VAL

LYS

4

VAL

LEU

ASP

CYS

ASP

THR

ILE

SER

GLN

ALA

5

LYS

GLU

LYS

MET

LEU

ASP

GLN

LEU

TYR

LYS

6

GLY

VAL

PRO

LEU

THR

GLN

ARG

PRO

ASP

PRO

7

ARG

THR

LEU

ASP

VAL

GLU

TRP

ARG

SER

GLY

8

VAL

ALA

GLY

HIS

LEU

ILE

LEU

SER

ASP

GLU

9

ASP

VAL

THR

SER

GLU

VAL

GLN

GLY

LEU

PHE

10

ARG

LEU

ASN

THR

LEU

GLN

HIS

TYR

LYS

11

VAL

PRO

ASP

GLY

ALA

THR

VAL

ALA

LEU

VAL

12

PRO

CYS

LEU

THR

LYS

HIS

VAL

LEU

ARG

GLU

13

ASN

LYS

Samples:

sample_1: RBD, [U-15N 100%], .75 mM; DTT 4 mM; MgCl2 4 mM; H2O 90%; D20 10%

sample_conditions_1: pH: 6.8; pressure: 1.0 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
15N-{1H} NOE	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
15N-{1H} NOE	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - peak intensities

Curvefit, Palmer - data analysis

ModelFree, Palmer - data analysis

NMR spectrometers:

Bruker DRX 600 MHz
Bruker DRX 800 MHz