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Found 1 Document (0.351 seconds)

BMRB: 34210

6F4Z

2'F-araG modified quadruplex with flipped G-tract and central tetrad

Authors

Dickerhoff, J., Weisz, K.

Assembly

DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*(GFL)P*GP*GP*AP*CP*GP*GP*G)-3')

Entity

1. DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*(GFL)P*GP*GP*AP*CP*GP*GP*G)-3') (polymer, Thiol state: not present), 22 monomers, 7053.452 Da Detail

GGGATGGGAC ACAGXGGACG GG

Formula weight

7053.452 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 69.4 %, Completeness (bb): 64.6 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	69.4 % (136 of 196)	69.4 % (136 of 196)
Suger, PO4	64.6 % (95 of 147)	64.6 % (95 of 147)
Nucleobase	83.7 % (41 of 49)	83.7 % (41 of 49)
Aromatic	95.2 % (40 of 42)	95.2 % (40 of 42)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. entity 1

GGGATGGGAC ACAGXGGACG GG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.37 mM DNA, 10 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA	natural abundance		0.37 mM
2	potassium phosphate	natural abundance		10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.37 mM DNA, 10 mM potassium phosphate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	DNA	natural abundance		0.37 mM
4	potassium phosphate	natural abundance		10 mM

Release date

2018-04-17

Citation

Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway
Dickerhoff, J., Weisz, K.
Chembiochem. (2018), 19, 927-930, PubMed 29460996 , DOI 10.1002/cbic.201800099 , Abstract

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34210_6f4z.nef
Input source #2: Coordindates	6f4z.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	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)
1:14:DG:O3'	1:15:GFL:P	unknown	unknown	n/a
1:15:GFL:O3'	1:16:DG:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	15	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--------20--
GGGATGGGACACAGXGGACGGG
||||||||||||||||||||||
GGGATGGGACACAGXGGACGGG

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_34210_6f4z.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	165		100.0 (chain: A, length: 22)
1	Distance restraints	CNS/XPLOR_distance_constraints_10	OK	184 (1)	noe	100.0 (chain: A, length: 22)
2	Distance restraints	CNS/XPLOR_distance_constraints_9	OK	48 (1)	hbond	63.6 (chain: A, length: 22)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_8	OK	18 (18)	.	81.8 (chain: A, length: 22)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 141
- ¹³C chemical shifts: 24

Completeness of assignments

Entity_assemble_ID: A

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
15	GFL

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	C8	140.75
2	DG	C8	138.283
3	DG	C8	136.696
4	DA	C2	155.078
4	DA	C8	141.959
5	DT	C6	137.923
6	DG	C8	141.656
7	DG	C8	140.166
8	DG	C8	137.713
9	DA	C2	154.783
9	DA	C8	141.509
10	DC	C6	143.495
11	DA	C2	154.676
11	DA	C8	141.422
13	DA	C8	141.444
14	DG	C8	141.868
16	DG	C8	136.72
17	DG	C8	138.311
18	DA	C8	142.229
19	DC	C6	142.967
20	DG	C8	141.227
21	DG	C8	140.774
22	DG	C8	138.638

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	196	136	69.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	147	95	64.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	41	83.7

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1	1	100.0
¹³C chemical shifts	1	0	0.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	22	100.0

Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_10
- 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: 184
- Weight of restraints: 1.0 (184)
- Potential type of restraints: square-well-parabolic (184)
- Range of distance target values: 2.9, 6.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_9
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 63.6%
  - Total number of restraints: 48
  - Weight of restraints: 1.0 (48)
  - Potential type of restraints: square-well-parabolic (48)
  - Range of distance target values: 1.95, 2.95 (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_8
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 81.8%
- Total number of restraints: 18
- Total number of restraints per polymer type: 18
- Weight of restraints: 1.0 (18)
- Potential type of restraints: square-well-parabolic (18)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords 2'F-ANA, DNA, G-QUADRUPLEX

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Found 1 Document (0.351 seconds)

BMRB: 34210

Sample #1

Sample #2

Experiments performed 5 experiments Detail

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Instrument

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NMR combined restraints 5 contents Detail