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BMRB: 18046

2LLF

Sixth Gelsolin-like domain of villin

Authors

Pfaff, D.A., Brockerman, J., Fedechkin, S., Burns, L., Zhang, F., McKnight, C., Smirnov, S.L.

Assembly

D6

Entity

1. D6 (polymer, Thiol state: all free), 107 monomers, 12416.61 Da Detail

PRLFECSNKT GRFLATEIVD FTQDDLDEND VYLLDTWDQI FFWIGKGANE SEKEAAAETA QEYLRSHPGS RDLDTPIIVV KQGFEPPTFT GWFMAWDPLC WSDRKSY

Formula weight

12416.61 Da

Source organism

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 84.7 %, Completeness (bb): 96.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.7 % (1077 of 1272)	83.0 % (546 of 658)	84.4 % (423 of 501)	95.6 % (108 of 113)
Backbone	96.8 % (610 of 630)	97.2 % (208 of 214)	95.6 % (301 of 315)	100.0 % (101 of 101)
Sidechain	76.0 % (565 of 743)	76.1 % (338 of 444)	76.7 % (220 of 287)	58.3 % (7 of 12)
Aromatic	58.9 % (99 of 168)	61.9 % (52 of 84)	53.2 % (42 of 79)	100.0 % (5 of 5)
Methyl	85.7 % (84 of 98)	85.7 % (42 of 49)	85.7 % (42 of 49)

1. D6

PRLFECSNKT GRFLATEIVD FTQDDLDEND VYLLDTWDQI FFWIGKGANE SEKEAAAETA QEYLRSHPGS RDLDTPIIVV KQGFEPPTFT GWFMAWDPLC WSDRKSY

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	H2O	natural abundance		50 M
9	D2O	[U-2H]		5 M
10	DTT	[U-2H]		10 mM
11	sodium azide	natural abundance		0.01 %
12	Calcium Chloride	natural abundance		5 mM
13	PIPES	[U-2H]		20 mM
14	D6	natural abundance		1 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
15	D2O	[U-2H]		55 M
16	DTT	[U-2H]		10 mM
17	sodium azide	natural abundance		0.01 %
18	Calcium Chloride	natural abundance		5 mM
19	PIPES	[U-2H]		20 mM
20	D6	natural abundance		1 mM

LACS Plot; CA

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.05 ppm, Outliers: 5 Detail

LACS Plot; CO

Referencing offset: 0.28 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LLF, Strand ID: A Detail

Release date

2012-11-04

Citation

Gelsolin-like activation of villin: calcium sensitivity of the long helix in domain 6
Fedechkin, S.O., Brockerman, J., Pfaff, D.A., Burns, L., Webb, T., Nelson, A., Zhang, F., Sabantsev, A.V., Melnikov, A.S., McKnight, C., Smirnov, S.L.
Biochemistry (2013), 52, 7890-7900, PubMed 24070253 , DOI 10.1021/bi400699s , Abstract

Related entities 1. D6, : 1 : 1 : 295 entities Detail

Interaction partners 1. D6, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

2 3D HNCACB

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

4 2D 1H-1H NOESY

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	H2O	natural abundance		50 M
9	D2O	[U-2H]		5 M
10	DTT	[U-2H]		10 mM
11	sodium azide	natural abundance		0.01 %
12	Calcium Chloride	natural abundance		5 mM
13	PIPES	[U-2H]		20 mM
14	D6	natural abundance		1 mM

5 3D HNHA

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

6 3D HNHB

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

8 3D 1H-15N TOCSY

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

10 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

12 3D HCCH-TOCSY

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

13 3D HCCH-COSY

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

14 HN(CA)CO

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

15 HNCO

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

16 2D 1H-1H TOCSY

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
15	D2O	[U-2H]		55 M
16	DTT	[U-2H]		10 mM
17	sodium azide	natural abundance		0.01 %
18	Calcium Chloride	natural abundance		5 mM
19	PIPES	[U-2H]		20 mM
20	D6	natural abundance		1 mM

17 2D 1H-1H NOESY

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
15	D2O	[U-2H]		55 M
16	DTT	[U-2H]		10 mM
17	sodium azide	natural abundance		0.01 %
18	Calcium Chloride	natural abundance		5 mM
19	PIPES	[U-2H]		20 mM
20	D6	natural abundance		1 mM

18 2D 1H-13C HSQC

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

19 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

20 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 720 MHz NHMFL,Florida State University, Tallahassee, FL

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	H2O	natural abundance		50 M
2	D2O	[U-2H]		5 M
3	DTT	[U-2H]		10 mM
4	sodium azide	natural abundance		0.01 %
5	Calcium Chloride	natural abundance		5 mM
6	PIPES	[U-2H]		20 mM
7	D6	[U-99% 13C; U-99% 15N]		1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18046_2llf.nef
Input source #2: Coordindates	2llf.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
PRLFECSNKTGRFLATEIVDFTQDDLDENDVYLLDTWDQIFFWIGKGANESEKEAAAETAQEYLRSHPGSRDLDTPIIVVKQGFEPPTFTGWFMAWDPLC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PRLFECSNKTGRFLATEIVDFTQDDLDENDVYLLDTWDQIFFWIGKGANESEKEAAAETAQEYLRSHPGSRDLDTPIIVVKQGFEPPTFTGWFMAWDPLC

-------
WSDRKSY
|||||||
WSDRKSY

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	107	0	0	100.0

Content subtype: combined_18046_2llf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1079		99.1 (chain: A, length: 107)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1209 (1)	noe	95.3 (chain: A, length: 107)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	402 (402)	.	100.0 (chain: A, length: 107)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 548
  - ¹³C chemical shifts: 423
  - ¹⁵N chemical shifts: 108
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 95.3%
- Total number of restraints: 1205
- Weight of restraints: 1.0 (1205)
- Potential type of restraints: upper-bound-parabolic (1205)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 100.0%
- Total number of restraints: 402
- Total number of restraints per polymer type: 402
- Weight of restraints: 1.0 (402)
- Potential type of restraints: square-well-parabolic (402)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords beta-core, CYANA, gelsolin-like domains, modular protein, NMR, villin