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BMRB: 25298

2MW4

Tetramerization domain of the Ciona intestinalis p53/p73-b transcription factor protein

Authors

Heering, J.P., Jonker, H.R.A., Loehr, F., Schwalbe, H., Doetsch, V.

Assembly

Tetramerization domain of the Ciona intestinalis p53/p73-b transcription factor protein

Entity

1. Tetramerization domain of the Ciona intestinalis p53/p73-b transcription factor protein (polymer, Thiol state: all free), 47 monomers, 5518.282 × 4 Da Detail

SDGDVVYTLN IRGKRKFEKV KEYKEALDLL DYVQPDVKKA CCQRNQI

Total weight

22073.129 Da

Max. entity weight

5518.282 Da

Source organism

Ciona intestinalis

Exptl. method

Refine. method

simulated annealing, energy minimization

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.7 %, Completeness (bb): 98.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.7 % (564 of 577)	97.7 % (299 of 306)	99.1 % (218 of 220)	92.2 % (47 of 51)
Backbone	98.6 % (276 of 280)	98.9 % (94 of 95)	98.6 % (137 of 139)	97.8 % (45 of 46)
Sidechain	97.4 % (333 of 342)	97.2 % (205 of 211)	100.0 % (126 of 126)	40.0 % (2 of 5)
Aromatic	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)
Methyl	100.0 % (50 of 50)	100.0 % (25 of 25)	100.0 % (25 of 25)

1. entity

SDGDVVYTLN IRGKRKFEKV KEYKEALDLL DYVQPDVKKA CCQRNQI

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 15N]		2.5 mM
2	L-arginine	natural abundance		50 mM
3	L-glutamate	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-100% 13C; U-100% 15N]		2.5 mM
8	L-arginine	natural abundance		50 mM
9	L-glutamate	natural abundance		50 mM
10	DTT	natural abundance		1 mM
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
13	entity	[U-100% 15N]		2 mM
14	entity	[U-100% 13C]		2 mM
15	L-arginine	natural abundance		50 mM
16	L-glutamate	natural abundance		50 mM
17	DTT	natural abundance		1 mM
18	H2O	natural abundance		95 %
19	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MW4, Strand ID: A, B, C, D Detail

Release date

2015-10-25

Citation

Structural investigations of the p53/p73 homologs from the tunicate species Ciona intestinalis reveal the sequence requirements for the formation of a tetramerization domain
Heering, J.P., Jonker, H.R.A., Loehr, F., Schwalbe, H., Doetsch, V.
Protein Sci. (2015), 25, 410-422, PubMed 26473758 , DOI 10.1002/pro.2830 , Abstract

Related entities 1. Tetramerization domain of the Ciona intestinalis p53/p73-b transcription factor protein, : 1 : 13 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 15N]		2.5 mM
2	L-arginine	natural abundance		50 mM
3	L-glutamate	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-100% 13C; U-100% 15N]		2.5 mM
8	L-arginine	natural abundance		50 mM
9	L-glutamate	natural abundance		50 mM
10	DTT	natural abundance		1 mM
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

3 3D HNCACB

Instrument

Bruker Avance - 900 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-100% 13C; U-100% 15N]		2.5 mM
8	L-arginine	natural abundance		50 mM
9	L-glutamate	natural abundance		50 mM
10	DTT	natural abundance		1 mM
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

4 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-100% 13C; U-100% 15N]		2.5 mM
8	L-arginine	natural abundance		50 mM
9	L-glutamate	natural abundance		50 mM
10	DTT	natural abundance		1 mM
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

5 3D HCCCONH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-100% 13C; U-100% 15N]		2.5 mM
8	L-arginine	natural abundance		50 mM
9	L-glutamate	natural abundance		50 mM
10	DTT	natural abundance		1 mM
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

6 3D CCCONH

Instrument

Bruker Avance - 600 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-100% 13C; U-100% 15N]		2.5 mM
8	L-arginine	natural abundance		50 mM
9	L-glutamate	natural abundance		50 mM
10	DTT	natural abundance		1 mM
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-100% 13C; U-100% 15N]		2.5 mM
8	L-arginine	natural abundance		50 mM
9	L-glutamate	natural abundance		50 mM
10	DTT	natural abundance		1 mM
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-100% 13C; U-100% 15N]		2.5 mM
8	L-arginine	natural abundance		50 mM
9	L-glutamate	natural abundance		50 mM
10	DTT	natural abundance		1 mM
11	H2O	natural abundance		95 %
12	D2O	natural abundance		5 %

9 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
13	entity	[U-100% 15N]		2 mM
14	entity	[U-100% 13C]		2 mM
15	L-arginine	natural abundance		50 mM
16	L-glutamate	natural abundance		50 mM
17	DTT	natural abundance		1 mM
18	H2O	natural abundance		95 %
19	D2O	natural abundance		5 %

10 3D 1H-13C NOESY 15N-edited inter

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
13	entity	[U-100% 15N]		2 mM
14	entity	[U-100% 13C]		2 mM
15	L-arginine	natural abundance		50 mM
16	L-glutamate	natural abundance		50 mM
17	DTT	natural abundance		1 mM
18	H2O	natural abundance		95 %
19	D2O	natural abundance		5 %

11 3D 1H-13C HMQC-NOESY-15N-1H-TROSY

Instrument

Bruker Avance - 900 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
13	entity	[U-100% 15N]		2 mM
14	entity	[U-100% 13C]		2 mM
15	L-arginine	natural abundance		50 mM
16	L-glutamate	natural abundance		50 mM
17	DTT	natural abundance		1 mM
18	H2O	natural abundance		95 %
19	D2O	natural abundance		5 %

12 3D 1H-13C NOESY J-resolved

Instrument

Bruker Avance - 700 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
13	entity	[U-100% 15N]		2 mM
14	entity	[U-100% 13C]		2 mM
15	L-arginine	natural abundance		50 mM
16	L-glutamate	natural abundance		50 mM
17	DTT	natural abundance		1 mM
18	H2O	natural abundance		95 %
19	D2O	natural abundance		5 %

13 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 15N]		2.5 mM
2	L-arginine	natural abundance		50 mM
3	L-glutamate	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25298_2mw4.nef
Input source #2: Coordindates	2mw4.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

-----110-------120-------130-------140---------
SDGDVVYTLNIRGKRKFEKVKEYKEALDLLDYVQPDVKKACCQRNQI
|||||||||||||||||||||||||||||||||||||||||||||||
SDGDVVYTLNIRGKRKFEKVKEYKEALDLLDYVQPDVKKACCQRNQI
--------10--------20--------30--------40-------

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

-----210-------220-------230-------240---------
SDGDVVYTLNIRGKRKFEKVKEYKEALDLLDYVQPDVKKACCQRNQI
|||||||||||||||||||||||||||||||||||||||||||||||
SDGDVVYTLNIRGKRKFEKVKEYKEALDLLDYVQPDVKKACCQRNQI
--------10--------20--------30--------40-------

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

-----310-------320-------330-------340---------
SDGDVVYTLNIRGKRKFEKVKEYKEALDLLDYVQPDVKKACCQRNQI
|||||||||||||||||||||||||||||||||||||||||||||||
SDGDVVYTLNIRGKRKFEKVKEYKEALDLLDYVQPDVKKACCQRNQI
--------10--------20--------30--------40-------

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

-----410-------420-------430-------440---------
SDGDVVYTLNIRGKRKFEKVKEYKEALDLLDYVQPDVKKACCQRNQI
|||||||||||||||||||||||||||||||||||||||||||||||
SDGDVVYTLNIRGKRKFEKVKEYKEALDLLDYVQPDVKKACCQRNQI
--------10--------20--------30--------40-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	47	0	0	100.0
B	B	47	0	0	100.0
C	C	47	0	0	100.0
D	D	47	0	0	100.0

Content subtype: combined_25298_2mw4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	561		100.0 (chain: A, length: 47)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1748 (1)	noe	100.0 (chain: A, length: 47), 40.4 (chain: B, length: 47), 31.9 (chain: C, length: 47)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	40 (1)	hbond	59.6 (chain: A, length: 47), 6.4 (chain: B, length: 47)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	60 (60)	.	76.6 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 297
  - ¹³C chemical shifts: 218
  - ¹⁵N chemical shifts: 46
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 47, Sequence coverage: 40.4%
  - Entity_assembly_ID: C, Chain length: 47, Sequence coverage: 31.9%
- Total number of restraints: 1744
- Weight of restraints: 1.0 (1744)
- Potential type of restraints: square-well-parabolic (1744)
- Range of distance target values: 1.2, 3.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 59.6%
    - Entity_assembly_ID: B, Chain length: 47, Sequence coverage: 6.4%
  - Total number of restraints: 40
  - Weight of restraints: 1.0 (40)
  - Potential type of restraints: square-well-parabolic (40)
  - Range of distance target values: 1.9, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
    - Chain_ID: D
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 76.6%
- Total number of restraints: 60
- Total number of restraints per polymer type: 60
- Weight of restraints: 1.0 (60)
- Potential type of restraints: square-well-parabolic (60)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ciona intestinalis, p53/p73-b, tetramerization domain, transcription factor