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BMRB: 16617

2KQY

Solution structure of Avian Thymic Hormone

Authors

Assembly

ATH

Entity

1. ATH (polymer, Thiol state: all free), 108 monomers, 11594.80 Da Detail

AITDILSAKD IESALSSCQA ADSFNYKSFF STVGLSSKTP DQIKKVFGIL DQDKSGFIEE EELQLFLKNF SSSARVLTSA ETKAFLAAGD TDGDGKIGVE EFQSLVKA

Formula weight

11594.8 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 94.5 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.5 % (1154 of 1221)	97.4 % (611 of 627)	90.2 % (433 of 480)	96.5 % (110 of 114)
Backbone	98.8 % (638 of 646)	98.6 % (219 of 222)	99.1 % (314 of 317)	98.1 % (105 of 107)
Sidechain	91.1 % (616 of 676)	96.8 % (392 of 405)	83.0 % (219 of 264)	71.4 % (5 of 7)
Aromatic	48.0 % (47 of 98)	85.7 % (42 of 49)	10.2 % (5 of 49)
Methyl	98.4 % (120 of 122)	98.4 % (60 of 61)	98.4 % (60 of 61)

1. ATH

AITDILSAKD IESALSSCQA ADSFNYKSFF STVGLSSKTP DQIKKVFGIL DQDKSGFIEE EELQLFLKNF SSSARVLTSA ETKAFLAAGD TDGDGKIGVE EFQSLVKA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
5	sodium chloride	natural abundance		150 (±0.3) mM
6	MES	natural abundance		10 (±0.2) mM
7	THP	natural abundance		5 (±0.2) mM
8	ATH	[U-15% 13C; U-98% 15N]		3 (±0.3) mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
9	sodium chloride	natural abundance		150 (±0.3) mM
10	MES	natural abundance		10 (±0.2) mM
11	THP	natural abundance		5 (±0.2) mM
12	ATH	[U-98% 15N]		3 (±0.3) mM

LACS Plot; CA

Referencing offset: 0.4 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.4 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.51 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KQY, Strand ID: A Detail

Release date

2010-03-21

Citation

Structure of avian thymic hormone, a high-affinity avian beta-parvalbumin, in the Ca2+-free and Ca2+-bound states
Schuermann, J.P., Tan, A., Tanner, J.J., Henzl, M.T.
J. Mol. Biol. (2010), 397, 991-1002, PubMed 20156445 , DOI 10.1016/j.jmb.2010.02.014 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P19753 released on 1991-02-01
Title PRVT_CHICK Entity Parvalbumin, thymic

Related entities 1. ATH, : 1 : 2 : 205 entities Detail

Experiments performed 17 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

3 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

4 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

7 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

8 3D HCACOCANH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

9 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

10 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

11 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

12 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

13 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

14 2D HBCBCGCDHD

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

15 2D HBCBCGCDCEHE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		150 (±0.3) mM
2	MES	natural abundance		10 (±0.2) mM
3	THP	natural abundance		5 (±0.2) mM
4	ATH	[U-98% 13C; U-98% 15N]		3 (±0.3) mM

16 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
5	sodium chloride	natural abundance		150 (±0.3) mM
6	MES	natural abundance		10 (±0.2) mM
7	THP	natural abundance		5 (±0.2) mM
8	ATH	[U-15% 13C; U-98% 15N]		3 (±0.3) mM

17 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.5) K, pH 6.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
5	sodium chloride	natural abundance		150 (±0.3) mM
6	MES	natural abundance		10 (±0.2) mM
7	THP	natural abundance		5 (±0.2) mM
8	ATH	[U-15% 13C; U-98% 15N]		3 (±0.3) mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16617_2kqy.nef
Input source #2: Coordindates	2kqy.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
AITDILSAKDIESALSSCQAADSFNYKSFFSTVGLSSKTPDQIKKVFGILDQDKSGFIEEEELQLFLKNFSSSARVLTSAETKAFLAAGDTDGDGKIGVE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AITDILSAKDIESALSSCQAADSFNYKSFFSTVGLSSKTPDQIKKVFGILDQDKSGFIEEEELQLFLKNFSSSARVLTSAETKAFLAAGDTDGDGKIGVE

--------
EFQSLVKA
||||||||
EFQSLVKA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_16617_2kqy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1147		99.1 (chain: A, length: 108)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2712 (1)	noe	99.1 (chain: A, length: 108)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	149 (132)	.	92.6 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 609
  - ¹³C chemical shifts: 428
  - ¹⁵N chemical shifts: 110
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 99.1%
- Total number of restraints: 2703
- Weight of restraints: 1.0 (2703)
- Potential type of restraints: upper-bound-parabolic (2703)
- Range of distance target values: 2.26, 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: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 92.6%
- Total number of restraints: 132
- Total number of restraints per polymer type: 132
- Weight of restraints: 1.0 (132)
- Potential type of restraints: square-well-parabolic (132)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords EF-HAND PROTEIN, metal-binding protein, parvalbumin