BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 26506

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   PubMed: 23214953

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

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).

Assembly members:
RBD, polymer, 122 residues, Formula weight is not available

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

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

Entity Sequences (FASTA):
RBD: KKDVEYRPLTLNALLAVGPG AGEAQGVPVKVLDCDTISQA KEKMLDQLYKGVPLTQRPDP RTLDVEWRSGVAGHLILSDE DVTSEVQGLFRRLNTLQHYK VPDGATVALVPCLTKHVLRE NK

Data sets:
Data typeCount
T1 relaxation values194
T2 relaxation values194
heteronuclear NOE values194
order parameters68

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Rho-GTPase Binding Domain1

Entities:

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

1   LYSLYSASPVALGLUTYRARGPROLEUTHR
2   LEUASNALALEULEUALAVALGLYPROGLY
3   ALAGLYGLUALAGLNGLYVALPROVALLYS
4   VALLEUASPCYSASPTHRILESERGLNALA
5   LYSGLULYSMETLEUASPGLNLEUTYRLYS
6   GLYVALPROLEUTHRGLNARGPROASPPRO
7   ARGTHRLEUASPVALGLUTRPARGSERGLY
8   VALALAGLYHISLEUILELEUSERASPGLU
9   ASPVALTHRSERGLUVALGLNGLYLEUPHE
10   ARGARGLEUASNTHRLEUGLNHISTYRLYS
11   VALPROASPGLYALATHRVALALALEUVAL
12   PROCYSLEUTHRLYSHISVALLEUARGGLU
13   ASNLYS

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
15N-{1H} NOEsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
15N-{1H} NOEsample_1isotropicsample_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

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