BMRBj - BMREntryMaster

Found 1 Document (0.782 seconds)

BMRB: 27144

5W77

DNA with compounds

Authors

Chen, X., Walters, K.J.

Assembly

c-Myc Pu22

Entity

1. c-Myc Pu22 (polymer, Thiol state: not present), 22 monomers, 7071.480 Da Detail

TGAGGGTGGG TAGGGTGGGT AA

2. 4-[(azepan-1-yl)methyl]-5-hydroxy-2-methyl-N-[4-(trifluoromethyl)phenyl]-1-benzofuran-3-carboxamide (non-polymer), 446.462 × 2 Da

Total weight

7964.404 Da

Max. entity weight

7071.48 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	97.0 % (197 of 203)	97.0 % (197 of 203)
Suger, PO4	100.0 % (154 of 154)	100.0 % (154 of 154)
Nucleobase	87.8 % (43 of 49)	87.8 % (43 of 49)
Aromatic	86.4 % (38 of 44)	86.4 % (38 of 44)
Methyl	100.0 % (5 of 5)	100.0 % (5 of 5)

1. c-Myc Pu22

TGAGGGTGGG TAGGGTGGGT AA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	c-Myc Pu22	natural abundance	0.3 mM
2	Tris	D11	25 mM
3	potassium chloride	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
4	c-Myc Pu22	natural abundance	.125 mM
5	DC34	natural abundance	.25 mM
6	Tris	D11	25 mM
7	potassium chloride	natural abundance	50 mM

Sample #3

Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
8	c-Myc Pu22	natural abundance	.25 mM
9	DC34	natural abundance	.5 mM
10	Tris	D11	25 mM
11	potassium chloride	natural abundance	50 mM

Sample #4

Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
12	c-Myc Pu22	natural abundance	.25 mM
13	DC34	selective 13C-labeling	.5 mM
14	Tris	D11	25 mM
15	potassium chloride	natural abundance	50 mM

Sample #5

Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	DC34	natural abundance	0.5 mM
17	Tris	D11	25 mM
18	potassium chloride	natural abundance	50 mM

Sample #6

Solvent system 90% H2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
19	c-Myc Pu22	natural abundance	.1 mM
20	DC34	natural abundance	0.0 ~ 0.6 mM
21	Tris	D11	25 mM
22	potassium chloride	natural abundance	50 mM

Release date

2017-06-18

Citation

DNA with compounds
Chen, X., Walters, K.J.
Nat. Commun. (2018), 9, PubMed , DOI 10.1038/s41467-018-06315-w

Experiments performed 16 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	c-Myc Pu22	natural abundance	0.3 mM
2	Tris	D11	25 mM
3	potassium chloride	natural abundance	50 mM

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
4	c-Myc Pu22	natural abundance	.125 mM
5	DC34	natural abundance	.25 mM
6	Tris	D11	25 mM
7	potassium chloride	natural abundance	50 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
8	c-Myc Pu22	natural abundance	.25 mM
9	DC34	natural abundance	.5 mM
10	Tris	D11	25 mM
11	potassium chloride	natural abundance	50 mM

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
4	c-Myc Pu22	natural abundance	.125 mM
5	DC34	natural abundance	.25 mM
6	Tris	D11	25 mM
7	potassium chloride	natural abundance	50 mM

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
8	c-Myc Pu22	natural abundance	.25 mM
9	DC34	natural abundance	.5 mM
10	Tris	D11	25 mM
11	potassium chloride	natural abundance	50 mM

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
4	c-Myc Pu22	natural abundance	.125 mM
5	DC34	natural abundance	.25 mM
6	Tris	D11	25 mM
7	potassium chloride	natural abundance	50 mM

7 2D 1H-1H COSY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
4	c-Myc Pu22	natural abundance	.125 mM
5	DC34	natural abundance	.25 mM
6	Tris	D11	25 mM
7	potassium chloride	natural abundance	50 mM

8 2D 1H-1H TOCSY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
8	c-Myc Pu22	natural abundance	.25 mM
9	DC34	natural abundance	.5 mM
10	Tris	D11	25 mM
11	potassium chloride	natural abundance	50 mM

9 2D 1H-1H COSY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
8	c-Myc Pu22	natural abundance	.25 mM
9	DC34	natural abundance	.5 mM
10	Tris	D11	25 mM
11	potassium chloride	natural abundance	50 mM

10 3D 13C half-filtered NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
12	c-Myc Pu22	natural abundance	.25 mM
13	DC34	selective 13C-labeling	.5 mM
14	Tris	D11	25 mM
15	potassium chloride	natural abundance	50 mM

11 2D 1H-1H COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	DC34	natural abundance	0.5 mM
17	Tris	D11	25 mM
18	potassium chloride	natural abundance	50 mM

12 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	DC34	natural abundance	0.5 mM
17	Tris	D11	25 mM
18	potassium chloride	natural abundance	50 mM

13 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	DC34	natural abundance	0.5 mM
17	Tris	D11	25 mM
18	potassium chloride	natural abundance	50 mM

14 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	DC34	natural abundance	0.5 mM
17	Tris	D11	25 mM
18	potassium chloride	natural abundance	50 mM

15 2D 1H-13C HMBC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% D2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	DC34	natural abundance	0.5 mM
17	Tris	D11	25 mM
18	potassium chloride	natural abundance	50 mM

16 1D 1H

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D6-DMSO, Pressure 1 atm, Temperature 298.2 K, pH 6.4

#	Name	Isotope labeling	Concentration
19	c-Myc Pu22	natural abundance	.1 mM
20	DC34	natural abundance	0.0 ~ 0.6 mM
21	Tris	D11	25 mM
22	potassium chloride	natural abundance	50 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_27144_5w77.nef
Input source #2: Coordindates	5w77.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:4:DG:O6	2:1:K:K	unknown	unknown	n/a
1:5:DG:O6	2:2:K:K	unknown	unknown	n/a
1:5:DG:O6	2:1:K:K	unknown	unknown	n/a
1:6:DG:O6	2:2:K:K	unknown	unknown	n/a
1:8:DG:O6	2:1:K:K	unknown	unknown	n/a
1:9:DG:O6	2:2:K:K	unknown	unknown	n/a
1:9:DG:O6	2:1:K:K	unknown	unknown	n/a
1:10:DG:O6	2:2:K:K	unknown	unknown	n/a
1:13:DG:O6	2:1:K:K	unknown	unknown	n/a
1:14:DG:O6	2:2:K:K	unknown	unknown	n/a
1:14:DG:O6	2:1:K:K	unknown	unknown	n/a
1:15:DG:O6	2:2:K:K	unknown	unknown	n/a
1:17:DG:O6	2:1:K:K	unknown	unknown	n/a
1:18:DG:O6	2:2:K:K	unknown	unknown	n/a
1:18:DG:O6	2:1:K:K	unknown	unknown	n/a
1:19:DG:O6	2:2:K:K	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	9WP	4-[(azepan-1-yl)methyl]-5-hydroxy-2-methyl-N-[4-(trifluoromethyl)phenyl]-1-benzofuran-3-carboxamide	None
B	2	9WP	4-[(azepan-1-yl)methyl]-5-hydroxy-2-methyl-N-[4-(trifluoromethyl)phenyl]-1-benzofuran-3-carboxamide	None
C	1	K	POTASSIUM ION	None
C	2	K	POTASSIUM ION	None

Sequence alignments

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

-----10--------20-----
TGAGGGTGGGTAGGGTGGGTAA
||||||||||||||||||||||
TGAGGGTGGGTAGGGTGGGTAA
--------10--------20--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	22	0	0	100.0

Content subtype: combined_27144_5w77.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	16		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	207		100.0 (chain: A, length: 22)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	933 (1)	noe	100.0 (chain: A, length: 22)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	54 (1)	hbond	54.5 (chain: A, length: 22)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	12 (12)	.	54.5 (chain: A, length: 22)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 207
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	203	197	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	154	154	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	43	87.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	21	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
- Total number of restraints: 927
- Weight of restraints: 1.0 (927)
- Potential type of restraints: square-well-parabolic (927)
- Range of distance target values: 2.4, 4.25 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 54.5%
  - Total number of restraints: 54
  - Weight of restraints: 1.0 (54)
  - Potential type of restraints: square-well-parabolic (54)
  - Range of distance target values: 1.96, 2.87 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
    - Chain_ID: C
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 54.5%
- Total number of restraints: 12
- Total number of restraints per polymer type: 12
- Weight of restraints: 1.0 (12)
- Potential type of restraints: square-well-parabolic (12)
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.782 seconds)

BMRB: 27144

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Experiments performed 16 experiments Detail

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NMR combined restraints 5 contents Detail