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BMRB: 25378

2MWZ

A structure of G-quadruplex

Authors

Cheong, V.V.V., Heddi, B., Lech, C.C.J., Phan, A.A.T.

Assembly

A G-quadruplex structure

Entity

1. A G-quadruplex structure (polymer, Thiol state: not present), 24 monomers, 7671.838 Da Detail

TTGGGTTAXG GTTAGGXTTA GGGA

Formula weight

7671.838 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.7 %, Completeness: 96.1 %, Completeness (bb): 100.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	96.1 % (198 of 206)	96.1 % (198 of 206)
Suger, PO4	100.0 % (154 of 154)	100.0 % (154 of 154)
Nucleobase	84.6 % (44 of 52)	84.6 % (44 of 52)
Aromatic	81.8 % (36 of 44)	81.8 % (36 of 44)
Methyl	100.0 % (8 of 8)	100.0 % (8 of 8)

1. DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3')

TTGGGTTAXG GTTAGGXTTA GGGA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPTPGPGPGPTPTPAP(8OG)PGPGPTPTPAPGPGP(3ZO)PTPTPAPGPGPGPA)-3')	natural abundance		0.7 mM
2	potassium phosphate	natural abundance		20 mM
3	potassium chloride	natural abundance		70 mM

Release date

2015-10-11

Citation

Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G·G·X·O tetrad
Cheong, V.V.V., Heddi, B., Lech, C.C.J., Phan, A.A.T.
Nucleic Acids Res. (2015), 43, 10506-10514, PubMed 26400177 , DOI 10.1093/nar/gkv826 , Abstract

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPTPGPGPGPTPTPAP(8OG)PGPGPTPTPAPGPGP(3ZO)PTPTPAPGPGPGPA)-3')	natural abundance		0.7 mM
2	potassium phosphate	natural abundance		20 mM
3	potassium chloride	natural abundance		70 mM

2 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPTPGPGPGPTPTPAP(8OG)PGPGPTPTPAPGPGP(3ZO)PTPTPAPGPGPGPA)-3')	natural abundance		0.7 mM
2	potassium phosphate	natural abundance		20 mM
3	potassium chloride	natural abundance		70 mM

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPTPGPGPGPTPTPAP(8OG)PGPGPTPTPAPGPGP(3ZO)PTPTPAPGPGPGPA)-3')	natural abundance		0.7 mM
2	potassium phosphate	natural abundance		20 mM
3	potassium chloride	natural abundance		70 mM

4 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPTPGPGPGPTPTPAP(8OG)PGPGPTPTPAPGPGP(3ZO)PTPTPAPGPGPGPA)-3')	natural abundance		0.7 mM
2	potassium phosphate	natural abundance		20 mM
3	potassium chloride	natural abundance		70 mM

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPTPGPGPGPTPTPAP(8OG)PGPGPTPTPAPGPGP(3ZO)PTPTPAPGPGPGPA)-3')	natural abundance		0.7 mM
2	potassium phosphate	natural abundance		20 mM
3	potassium chloride	natural abundance		70 mM

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(TPTPGPGPGPTPTPAP(8OG)PGPGPTPTPAPGPGP(3ZO)PTPTPAPGPGPGPA)-3')	natural abundance		0.7 mM
2	potassium phosphate	natural abundance		20 mM
3	potassium chloride	natural abundance		70 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25378_2mwz.nef
Input source #2: Coordindates	2mwz.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)
1:8:DA:O3'	1:9:8OG:P	unknown	unknown	n/a
1:9:8OG:O3'	1:10:DG:P	unknown	unknown	n/a
1:16:DG:O3'	1:17:3ZO:P	unknown	unknown	n/a
1:17:3ZO:O3'	1:18:DT:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	9	8OG	8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	17	3ZO	2'-DEOXY-XANTHOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20----
TTGGGTTAXGGTTAGGXTTAGGGA
||||||||||||||||||||||||
TTGGGTTAXGGTTAGGXTTAGGGA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	24	0	0	100.0

Content subtype: combined_25378_2mwz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	232		100.0 (chain: A, length: 24)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	553 (1)	noe	95.8 (chain: A, length: 24)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	55 (1)	hbond	62.5 (chain: A, length: 24)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	11 (11)	.	45.8 (chain: A, length: 24)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 232
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 95.8%
- Total number of restraints: 551
- Weight of restraints: 1.0 (551)
- Potential type of restraints: square-well-parabolic (551)
- Range of distance target values: 2.0, 6.88 (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_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 24, Sequence coverage: 62.5%
  - Total number of restraints: 55
  - Weight of restraints: 1.0 (55)
  - Potential type of restraints: square-well-parabolic (55)
  - Range of distance target values: 1.95, 3.15 (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: 24, Sequence coverage: 45.8%
- Total number of restraints: 11
- Total number of restraints per polymer type: 11
- Weight of restraints: 1.0 (11)
- Potential type of restraints: square-well-parabolic (11)
- Dihedral angle restraints per residue

Keywords 8-oxoguanine, G-quadruplex, GGXO, Xanthine, xanthosine