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BMRB: 19784

2MKM

Solution structure of the G-triplex truncated-TBA

Authors

Cerofolini, L., Fragai, M., Giachetti, A., Limongelli, V., Luchinat, C., Novellino, E., Parrinello, M., Randazzo, A.

Assembly

G-triplex truncated-TBA

Entity

1. G-triplex truncated-TBA (polymer, Thiol state: not present), 11 monomers, 3539.226 Da Detail

GGTTGGTGTG G

Formula weight

3539.226 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.4 %, Completeness (bb): 97.7 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	97.4 % (111 of 114)	99.0 % (102 of 103)	81.8 % (9 of 11)
Suger, PO4	97.7 % (86 of 88)	100.0 % (77 of 77)	81.8 % (9 of 11)
Nucleobase	96.2 % (25 of 26)	96.2 % (25 of 26)
Aromatic	95.5 % (21 of 22)	95.5 % (21 of 22)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*G)-3')

GGTTGGTGTG G

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Release date

2014-11-16

Citation

G-triplex structure and formation propensity
Cerofolini, L., Fragai, M., Giachetti, A., Limongelli, V., Luchinat, C., Novellino, E., Parrinello, M., Randazzo, A.
Nucleic Acids Res. (2014), 42, 13393-13404, PubMed 25378342 , DOI 10.1093/nar/gku1084 , Abstract

Experiments performed 10 experiments Detail

1 2D DQF-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 2D 1H-1H ROESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 2D JR-HMBC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 E.COSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 2D 31P-1H HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 2D 31P-1H COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 2D 13C-1H HSQC

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

10 IPAP

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 274 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(GPGPTPTPGPGPTPGPTPGP*G)-3')	natural abundance		0.7 mM
2	potassium chloride	natural abundance		70 mM
3	potassium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.2 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19784_2mkm.nef
Input source #2: Coordindates	2mkm.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-
GGTTGGTGTGG
|||||||||||
GGTTGGTGTGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	11	0	0	100.0

Content subtype: combined_19784_2mkm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	186		100.0 (chain: A, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_7	Warning	315 (1)	noe	100.0 (chain: A, length: 11)
2	Distance restraints	CNS/XPLOR_distance_constraints_8	Warning	25 (1)	hbond	54.5 (chain: A, length: 11)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_9	OK	67 (67)	.	100.0 (chain: A, length: 11)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_10	OK	35 (35)	.	100.0 (chain: A, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 111
- ¹³C chemical shifts: 66
- ³¹P chemical shifts: 9

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H22	9.716
1	DG	H21	6.145
1	DG	C1'	90.26
1	DG	C2'	40.793
1	DG	C3'	81.407
1	DG	C4'	88.932
1	DG	C5'	64.008
1	DG	C8	141.157
2	DG	H22	6.901
2	DG	C1'	83.892
2	DG	C2'	37.823
2	DG	C3'	80.03
2	DG	C4'	87.095
2	DG	C5'	67.759
2	DG	C8	139.365
2	DG	P	-0.622
3	DT	C2'	39.69
3	DT	C3'	78.278
3	DT	C4'	86.103
3	DT	C5'	67.688
3	DT	C6	137.727
3	DT	C7	13.699
3	DT	P	-2.152
4	DT	C1'	86.751
4	DT	C2'	38.995
4	DT	C3'	77.757
4	DT	C4'	86.067
4	DT	C5'	66.658
4	DT	C6	140.307
4	DT	C7	13.68
4	DT	P	-1.576
5	DG	H22	7.17
5	DG	C1'	88.321
5	DG	C2'	34.086
5	DG	C3'	80.367
5	DG	C4'	88.987
5	DG	C5'	69.471
5	DG	C8	142.928
5	DG	P	-0.538
6	DG	H22	6.91
6	DG	C1'	83.768
6	DG	C2'	39.406
6	DG	C4'	87.164
6	DG	C5'	68.069
6	DG	C8	138.624
6	DG	P	-0.901
7	DT	C1'	84.551
7	DT	C2'	39.011
7	DT	C3'	74.404
7	DT	C4'	84.14
7	DT	C5'	64.57
7	DT	C6	136.08
7	DT	C7	14.693
7	DT	P	-1.146
8	DG	H22	5.899
8	DG	C1'	85.665
8	DG	C2'	39.885
8	DG	C3'	79.54
8	DG	C4'	88.647
8	DG	C5'	68.33
8	DG	C8	139.237
8	DG	P	-1.376
9	DT	C1'	88.617
9	DT	C2'	42.958
9	DT	C4'	89.313
9	DT	C5'	67.742
9	DT	C6	137.803
9	DT	C7	14.062
10	DG	H22	6.483
10	DG	C1'	89.425
10	DG	C2'	39.676
10	DG	C3'	80.099
10	DG	C4'	88.532
10	DG	C8	142.468
10	DG	P	-0.049
11	DG	H22	10.124
11	DG	H21	6.905
11	DG	C1'	83.604
11	DG	C2'	41.63
11	DG	C3'	72.038
11	DG	C4'	86.87
11	DG	C5'	63.781
11	DG	C8	139.035
11	DG	P	-0.862

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	103	102	99.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	77	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	25	96.2

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_7
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 314
- Weight of restraints: 1.0 (314)
- Potential type of restraints: square-well-parabolic (314)
- Range of distance target values: 1.9, 3.75 (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: CNS/XPLOR_distance_constraints_8
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 54.5%
  - Total number of restraints: 25
  - Weight of restraints: 1.0 (25)
  - Potential type of restraints: square-well-parabolic (25)
  - Range of distance target values: 1.8, 7.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_9
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 67
- Total number of restraints per polymer type: 67
- Weight of restraints: 1.0 (67)
- Potential type of restraints: square-well-parabolic (67)
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_10
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 35
- Potential type of restraints: undefined (35)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords DNA, G-triad, G-triplex, solution NMR, Structure, truncated-TBA