BMRB Entry 18046

Name: Sixth Gelsolin-like domain of villin
Published: 2012-11-05

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PDB ID: 2llf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18046
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:

Sixth Gelsolin-like domain of villin

Deposition date:

2011-11-07

Original release date:

2012-11-05

Authors:

Pfaff, Danielle; Brockerman, Jacob; Fedechkin, Stanislav; Burns, Lucian; Zhang, Fengli; McKnight, C. James; Smirnov, Serge

Citation:

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).
PubMed: 24070253

Assembly members:

Assembly members:
D6, polymer, 107 residues, 12427.814 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET31

Entity Sequences (FASTA):

Entity Sequences (FASTA):
D6: PRLFECSNKTGRFLATEIVD FTQDDLDENDVYLLDTWDQI FFWIGKGANESEKEAAAETA QEYLRSHPGSRDLDTPIIVV KQGFEPPTFTGWFMAWDPLC WSDRKSY

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	423
15N chemical shifts	108
1H chemical shifts	631

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	D6	1

Entities:

Entity 1, D6 107 residues - 12427.814 Da.

Corresponds to 107 residue polypeptide from villin [gallus gallus] starting at position 619 and ending at 725

1

PRO

ARG

LEU

PHE

GLU

CYS

SER

ASN

LYS

THR

2

GLY

ARG

PHE

LEU

ALA

THR

GLU

ILE

VAL

ASP

3

PHE

THR

GLN

ASP

LEU

ASP

GLU

ASN

ASP

4

VAL

TYR

LEU

ASP

THR

TRP

ASP

GLN

ILE

5

PHE

TRP

ILE

GLY

LYS

GLY

ALA

ASN

GLU

6

SER

GLU

LYS

GLU

ALA

GLU

THR

ALA

7

GLN

GLU

TYR

LEU

ARG

SER

HIS

PRO

GLY

SER

8

ARG

ASP

LEU

ASP

THR

PRO

ILE

VAL

9

LYS

GLN

GLY

PHE

GLU

PRO

THR

PHE

THR

10

GLY

TRP

PHE

MET

ALA

TRP

ASP

PRO

LEU

CYS

11

TRP

SER

ASP

ARG

LYS

SER

TYR

Samples:

sample_1: H2O 50 M; D2O, [U-2H], 5 M; DTT, [U-2H], 10 mM; sodium azide 0.01%; Calcium Chloride 5 mM; PIPES, [U-2H], 20 mM; D6, [U-99% 13C; U-99% 15N], 1 mM

sample_2: H2O 50 M; D2O, [U-2H], 5 M; DTT, [U-2H], 10 mM; sodium azide 0.01%; Calcium Chloride 5 mM; PIPES, [U-2H], 20 mM; D6 1 mM

sample_3: D2O, [U-2H], 55 M; DTT, [U-2H], 10 mM; sodium azide 0.01%; Calcium Chloride 5 mM; PIPES, [U-2H], 20 mM; D6 1 mM

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 273 K

sample_conditions_2: pH: 7; pressure: 1 atm; temperature: 273 K

sample_conditions_3: pH: 7; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
HN(CA)CO	sample_1	isotropic	sample_conditions_1
HNCO	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMRView v5.2.2, Johnson, One Moon Scientific - peak picking

NMRPipe v5.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

PREDITOR v1.0, Berjanskii MV, Neal S, Wishart DS - dihedral prediction, geometry optimization, structure solution

NMR spectrometers:

Varian INOVA 720 MHz
Varian INOVA 500 MHz