BMRBj - BMREntryMaster

Found 1 Document (0.388 seconds)

BMRB: 19386

2MB2

parallel-stranded G-quadruplex in DNA poly-G stretches

Authors

Sengar, A., Heddi, B., Phan, A.

Assembly

parallel-stranded G-quadruplex in DNA poly-G stretches

Entity

1. parallel-stranded G-quadruplex in DNA poly-G stretches (polymer, Thiol state: not present), 18 monomers, 5868.679 Da Detail

TTGGGGGGGG GGGGGGGT

Formula weight

5868.679 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.8 %, Completeness (bb): 99.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	95.8 % (158 of 165)	95.8 % (158 of 165)
Suger, PO4	99.2 % (125 of 126)	99.2 % (125 of 126)
Nucleobase	84.6 % (33 of 39)	84.6 % (33 of 39)
Aromatic	83.3 % (30 of 36)	83.3 % (30 of 36)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. DNA (5'-D(*TP*TP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*T)-3')

TTGGGGGGGG GGGGGGGT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(TPTPGPGPGPGPGPGPGPGPGPGPGPGPGPGPGPT)-3')	natural abundance	0.1 ~ 2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	KCl	natural abundance	5 mM
5	KPi	natural abundance	5 mM

Release date

2014-11-30

Citation

Formation of G-quadruplexes in poly-G sequences: structure of a propeller-type parallel-stranded G-quadruplex formed by a G₁₅ stretch
Sengar, A., Heddi, B., Phan, A.
Biochemistry (2014), 53, 7718-7723, PubMed 25375976 , DOI 10.1021/bi500990v , Abstract

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19386_2mb2.nef
Input source #2: Coordindates	2mb2.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--------
TTGGGGGGGGGGGGGGGT
||||||||||||||||||
TTGGGGGGGGGGGGGGGT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	18	0	0	100.0

Content subtype: combined_19386_2mb2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	164		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	320 (1)	noe	100.0 (chain: A, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	48 (1)	hbond	66.7 (chain: A, length: 18)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	12 (12)	.	66.7 (chain: A, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 164
- 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	165	158	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	125	99.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	33	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 318
- Weight of restraints: 1.0 (318)
- Potential type of restraints: square-well-parabolic (318)
- Range of distance target values: 2.0, 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_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 66.7%
  - Total number of restraints: 48
  - Weight of restraints: 1.0 (48)
  - Potential type of restraints: square-well-parabolic (48)
  - Range of distance target values: 1.99, 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 66.7%
- 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

Keywords G-quadruplex, G-tracts, NMR, poly-G stretches, propeller structure

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.388 seconds)

BMRB: 19386

Sample

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail