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BMRB: 19017

2M4P

Solution structure of an intramolecular propeller-type G-quadruplex containing a single bulge

Authors

Thachappilly Mukundan, V.

Assembly

Bulges in G-quadruplexes

Entity

1. Bulges in G-quadruplexes (polymer, Thiol state: not present), 19 monomers, 6097.833 Da Detail

TTGTGGTGGG TGGGTGGGT

Formula weight

6097.833 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.9 %, Completeness (bb): 98.5 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	94.9 % (169 of 178)	94.9 % (169 of 178)
Suger, PO4	98.5 % (131 of 133)	98.5 % (131 of 133)
Nucleobase	84.4 % (38 of 45)	84.4 % (38 of 45)
Aromatic	81.6 % (31 of 38)	81.6 % (31 of 38)
Methyl	100.0 % (7 of 7)	100.0 % (7 of 7)

1. DNA 1

TTGTGGTGGG TGGGTGGGT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	DNA_1	natural abundance	0.1 ~ 2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Potassium Ion	natural abundance	60 mM

Release date

2013-05-29

Citation

Bulges in G-quadruplexes: broadening the definition of G-quadruplex-forming sequences
Mukundan, V., Phan, A.
J. Am. Chem. Soc. (2013), 135, 5017-5028, PubMed 23521617 , DOI 10.1021/ja310251r , Abstract

Experiments performed 4 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19017_2m4p.nef
Input source #2: Coordindates	2m4p.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---------
TTGTGGTGGGTGGGTGGGT
|||||||||||||||||||
TTGTGGTGGGTGGGTGGGT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	19	0	0	100.0

Content subtype: combined_19017_2m4p.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	169		100.0 (chain: A, length: 19)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	326 (1)	noe	100.0 (chain: A, length: 19)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	29 (1)	noe	78.9 (chain: A, length: 19)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	18 (1)	noe	89.5 (chain: A, length: 19)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	30 (30)	.	63.2 (chain: A, length: 19)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 169
- 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	178	169	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	133	131	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	38	84.4

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of restraints: 325
- Weight of restraints: 1.0 (325)
- Potential type of restraints: square-well-parabolic (325)
- Range of distance target values: 2.08, 6.75 (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_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 78.9%
  - Total number of restraints: 29
  - Weight of restraints: 1.0 (29)
  - Potential type of restraints: square-well-parabolic (29)
  - Range of distance target values: 2.9, 5.75 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 89.5%
    - Total number of restraints: 18
    - Weight of restraints: 1.0 (18)
    - Potential type of restraints: square-well-parabolic (18)
    - Range of distance target values: 42.15, 42.15 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - 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: 19, Sequence coverage: 63.2%
- Total number of restraints: 30
- Total number of restraints per polymer type: 30
- Weight of restraints: 1.0 (30)
- Potential type of restraints: square-well-parabolic (30)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords G-quadruplex, Bulges

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Found 1 Document (0.364 seconds)

BMRB: 19017

Sample

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail