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 19497

Title: calcium-free V6 domain of villin   PubMed: 24070253

Deposition date: 2013-09-16 Original release date: 2014-04-15

Authors: Serge, Smirnov

Citation: Fedechkin, Stanislav; Brockerman, Jacob; Pfaff, Danielle; Burns, Lucian; Webb, Terry; Nelson, Alexander; Zhang, Fengli; Sabantsev, Anton; Melnikov, Alexey; McKnight, C. James; Smirnov, Serge. "Gelsolin-like activation of villin: calcium sensitivity of the long helix in domain 6."  Biochemistry 52, 7890-7900 (2013).

Assembly members:
Villin_domain_6, polymer, 107 residues, 12427.814 Da.

Natural source:   Common Name: chicken   Taxonomy ID: 9031   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Gallus gallus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET24a

Entity Sequences (FASTA):
Villin_domain_6: PRLFECSNKTGRFLATEIVD FTQDDLDENDVYLLDTWDQI FFWIGKGANESEKEAAAETA QEYLRSHPGSRDLDTPIIVV KQGFEPPTFTGWFMAWDPLC WSDRKSY

Data sets:
Data typeCount
13C chemical shifts321
15N chemical shifts100
1H chemical shifts384

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1Ca free domain 6 of villin1

Entities:

Entity 1, Ca free domain 6 of villin 107 residues - 12427.814 Da.

1   PROARGLEUPHEGLUCYSSERASNLYSTHR
2   GLYARGPHELEUALATHRGLUILEVALASP
3   PHETHRGLNASPASPLEUASPGLUASNASP
4   VALTYRLEULEUASPTHRTRPASPGLNILE
5   PHEPHETRPILEGLYLYSGLYALAASNGLU
6   SERGLULYSGLUALAALAALAGLUTHRALA
7   GLNGLUTYRLEUARGSERHISPROGLYSER
8   ARGASPLEUASPTHRPROILEILEVALVAL
9   LYSGLNGLYPHEGLUPROPROTHRPHETHR
10   GLYTRPPHEMETALATRPASPPROLEUCYS
11   TRPSERASPARGLYSSERTYR

Samples:

sample_1: Villin domain 6, [U-95% 13C; U-95% 15N], 0.5 mM; sodium azide 0.01%; PIPES, [U-99% 2H], 20 mM; DTT 5 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCBsample_1isotropicsample_conditions_1
3D HACONHsample_1isotropicsample_conditions_1
3D CBCACONHsample_1isotropicsample_conditions_1
3D HNCOCAsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1

Software:

VNMRJ v2.2C, Varian - collection

ADAPT-NMR v2, Lee W, Hu K, Tonelli M, Bahrami A, Neuhardt E, Glass KC, Markley JL - chemical shift assignment, peak picking

CS23D v2, Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G. - structure solution

Chiron, Ramachandran, S., Kota, P., Ding, F. and Dokholyan, N. V. - refinement

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

NMR spectrometers:

  • Varian DirectDrive 700 MHz

Related Database Links:

BMRB 15097 18046
PDB

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