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BMRB: 18012

2LKT

Solution structure of N-terminal domain of human TIG3

Authors

Wang, L., Yu, W., Xia, B.

Assembly

N-terminal domain of human TIG3

Entity

1. N-terminal domain of human TIG3 (polymer, Thiol state: all free), 125 monomers, 14032.73 Da Detail

MASPHQEPKP GDLIEIFRLG YEHWALYIGD GYVIHLAPPS EYPGAGSSSV FSVLSNSAEV KRERLEDVVG GCCYRVNNSL DHEYQPRPVE VIISSAKEMV GQKMKYSIVS RNCEHFVTQL RYGKS

Formula weight

14032.73 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.0 %, Completeness: 79.5 %, Completeness (bb): 86.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.5 % (1149 of 1446)	78.2 % (590 of 754)	80.2 % (454 of 566)	83.3 % (105 of 126)
Backbone	86.5 % (635 of 734)	85.7 % (216 of 252)	87.9 % (321 of 365)	83.8 % (98 of 117)
Sidechain	75.0 % (620 of 827)	74.7 % (375 of 502)	75.3 % (238 of 316)	77.8 % (7 of 9)
Aromatic	28.6 % (36 of 126)	47.6 % (30 of 63)	8.1 % (5 of 62)	100.0 % (1 of 1)
Methyl	91.0 % (111 of 122)	90.2 % (55 of 61)	91.8 % (56 of 61)

1. entity

MASPHQEPKP GDLIEIFRLG YEHWALYIGD GYVIHLAPPS EYPGAGSSSV FSVLSNSAEV KRERLEDVVG GCCYRVNNSL DHEYQPRPVE VIISSAKEMV GQKMKYSIVS RNCEHFVTQL RYGKS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

Protein Blocks Logo

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

Release date

2012-02-09

Citation

1H, 13C, and 15N resonance assignments of the N-terminal domain of human TIG3
Wang, L., Yu, W., Ren, X., Lin, J., Jin, C., Xia, B.
Biomol. NMR Assign. (2012), 6, 201-203, PubMed 22290676 , DOI 10.1007/s12104-012-9357-2 , Abstract

Related entities 1. N-terminal domain of human TIG3, : 1 : 3 : 1 : 65 entities Detail

Interaction partners 1. N-terminal domain of human TIG3, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz Bruker Avance 800 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

2 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz Bruker Avance 800 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

3 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz Bruker Avance 800 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

4 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz Bruker Avance 800 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz Bruker Avance 500 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

6 3D HNCACB

Instrument

Bruker Avance - 500 MHz Bruker Avance 500 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz Bruker Avance 500 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

8 3D HNCO

Instrument

Bruker Avance - 500 MHz Bruker Avance 500 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

9 3D HNCA

Instrument

Bruker Avance - 500 MHz Bruker Avance 500 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

10 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz Bruker Avance 500 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz Bruker Avance 500 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

12 3D HCCH-COSY

Instrument

Bruker Avance - 500 MHz Bruker Avance 500 MHz spectrometer with a cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	TIG3N protein	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		20 mM
5	urea	natural abundance		2 M
6	H2O	natural abundance		95 %
7	D2O	[U-2H]		5 %
8	DSS	natural abundance		0.01 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18012_2lkt.nef
Input source #2: Coordindates	2lkt.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
MASPHQEPKPGDLIEIFRLGYEHWALYIGDGYVIHLAPPSEYPGAGSSSVFSVLSNSAEVKRERLEDVVGGCCYRVNNSLDHEYQPRPVEVIISSAKEMV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MASPHQEPKPGDLIEIFRLGYEHWALYIGDGYVIHLAPPSEYPGAGSSSVFSVLSNSAEVKRERLEDVVGGCCYRVNNSLDHEYQPRPVEVIISSAKEMV

-------110-------120-----
GQKMKYSIVSRNCEHFVTQLRYGKS
|||||||||||||||||||||||||
GQKMKYSIVSRNCEHFVTQLRYGKS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_18012_2lkt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1164		95.2 (chain: A, length: 125)
1	Distance restraints	AMBER_distance_constraints_6	Warning	9859 (1)	noe	92.0 (chain: A, length: 125)
2	Distance restraints	AMBER_distance_constraints_5	OK	82 (1)	hbond	44.8 (chain: A, length: 125)
1	Dihedral angle restraints	AMBER_dihedral_2	OK	155 (155)	.	81.6 (chain: A, length: 125)
2	Dihedral angle restraints	AMBER_dihedral_4	Warning	1 (1)	.	1.6 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 95.2%
- Total number of assignments
  - ¹H chemical shifts: 609
  - ¹³C chemical shifts: 452
  - ¹⁵N chemical shifts: 103
- 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: AMBER_distance_constraints_6
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 92.0%
- Total number of restraints: 9676
- Weight of restraints: 1.0 (9676)
- Potential type of restraints: square-well-parabolic (9676)
- Range of distance target values: 2.67, 8.77 (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
- Saveframe: AMBER_distance_constraints_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 44.8%
  - Total number of restraints: 82
  - Weight of restraints: 1.0 (82)
  - Potential type of restraints: square-well-parabolic (82)
  - Range of distance target values: 2.42, 3.27 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 81.6%
- Total number of restraints: 155
- Total number of restraints per polymer type: 155
- Weight of restraints: 1.0 (155)
- Potential type of restraints: square-well-parabolic (155)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: AMBER_dihedral_4
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 1.6%
  - Total number of restraints: 1
  - Total number of restraints per polymer type: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Dihedral angle restraints per residue

Keywords human tumor suppressor II family, NlpC/P60, NMR structure, TIG3