BMRBj - BMREntryMaster

Found 1 Document (0.353 seconds)

BMRB: 25651

2N3M

Isolation and structural characterization of an active G-quadruplex motif from AGRO100

Authors

Chung, W., Heddi, B., Phan, A.

Assembly

active G-quadruplex motif from AGRO100

Entity

1. active G-quadruplex motif from AGRO100 (polymer, Thiol state: not present), 28 monomers, 8935.619 Da Detail

TGGTGGTGGT TGTTGTGGTG GTGGTGGT

Formula weight

8935.619 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 84.5 %, Completeness (bb): 85.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	84.5 % (223 of 264)	84.5 % (223 of 264)
Suger, PO4	85.2 % (167 of 196)	85.2 % (167 of 196)
Nucleobase	82.4 % (56 of 68)	82.4 % (56 of 68)
Aromatic	78.6 % (44 of 56)	78.6 % (44 of 56)
Methyl	100.0 % (12 of 12)	100.0 % (12 of 12)

1. DNA (28-MER)

TGGTGGTGGT TGTTGTGGTG GTGGTGGT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (28-MER)	natural abundance	1.2 ~ 2.0 mM
2	KPi	natural abundance	20 mM
3	KCl	natural abundance	70 mM
4	H20	natural abundance	90 %
5	D20	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (28-MER)	[U-2% 15N]	0.2 ~ 1.0 mM
7	KPi	natural abundance	20 mM
8	KCl	natural abundance	70 mM
9	H20	natural abundance	90 %
10	D20	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
11	DNA (28-MER)	natural abundance	1.2 ~ 2.0 mM
12	KPi	natural abundance	20 mM
13	KCl	natural abundance	70 mM
14	D20	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
15	DNA (28-MER)	[U-100% 2H]	0.2 ~ 1.0 mM
16	KPi	natural abundance	20 mM
17	KCl	natural abundance	70 mM
18	D20	natural abundance	100 %

Release date

2016-07-04

Citation

Isolation and structural characterization of an active G-quadruplex motif from AGRO100
Chung, W., Heddi, B., Phan, A.
Not known

Experiments performed 6 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25651_2n3m.nef
Input source #2: Coordindates	2n3m.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--------20--------
TGGTGGTGGTTGTTGTGGTGGTGGTGGT
||||||||||||||||||||||||||||
TGGTGGTGGTTGTTGTGGTGGTGGTGGT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	28	0	0	100.0

Content subtype: combined_25651_2n3m.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	247		100.0 (chain: A, length: 28)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	386 (1)	noe	100.0 (chain: A, length: 28)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	20 (1)	undefined	64.3 (chain: A, length: 28)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	64 (1)	hbond	57.1 (chain: A, length: 28)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	16 (16)	.	57.1 (chain: A, length: 28)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 247
- 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	264	223	84.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	196	167	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	56	82.4

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	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: 28, Sequence coverage: 100.0%
- Total number of restraints: 386
- Weight of restraints: 1.0 (386)
- Potential type of restraints: square-well-parabolic (386)
- Range of distance target values: 2.4, 6.25 (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: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 64.3%
  - Total number of restraints: 20
  - Weight of restraints: 1.0 (20)
  - Potential type of restraints: square-well-parabolic (20)
  - Range of distance target values: 12.0, 12.5 (Å)
  - Histogram of 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: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 57.1%
    - Total number of restraints: 64
    - Weight of restraints: 1.0 (64)
    - Potential type of restraints: square-well-parabolic (64)
    - Range of distance target values: 2.0, 2.9 (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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 28, Sequence coverage: 57.1%
- Total number of restraints: 16
- Total number of restraints per polymer type: 16
- Weight of restraints: 1.0 (16)
- Potential type of restraints: square-well-parabolic (16)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords AGRO100, AS1411, DNA, G-quadruplex, NMR

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 (0.353 seconds)

BMRB: 25651

Sample #1

Sample #2

Sample #3

Sample #4

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail