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Found 1 Document (0.565 seconds)

BMRB: 18524

2LUJ

Solution structure of a parallel-stranded oligoisoguanine DNA pentaplex formed by d(T(iG)4T) in the presence of Cs ions

Authors

Kang, M., Heuberger, B., Chaput, J.C., Switzer, C., Feigon, J.

Assembly

DNA OUH

Entity

1. DNA OUH (polymer, Thiol state: not present), 6 monomers, 1943.224 × 5 Da Detail

TXXXXT

Total weight

9716.12 Da

Max. entity weight

1943.224 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 33.3 %, Completeness: 85.0 %, Completeness (bb): 92.9 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	85.0 % (17 of 20)	85.0 % (17 of 20)
Suger, PO4	92.9 % (13 of 14)	92.9 % (13 of 14)
Nucleobase	66.7 % (4 of 6)	66.7 % (4 of 6)
Aromatic	50.0 % (2 of 4)	50.0 % (2 of 4)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

1. DNA OUH

TXXXXT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	DNA	natural abundance	0.7 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
4	DNA	natural abundance		0.7 mM
5	D2O	natural abundance		100 %

Release date

2012-06-18

Citation

Solution structure of a parallel-stranded oligoisoguanine DNA pentaplex formed by d(T(iG)4 T) in the presence of Cs+ ions
Kang, M., Heuberger, B., Chaput, J.C., Switzer, C., Feigon, J.
Angew. Chem Int Ed Engl. (2012), 51, 7952-7955, PubMed 22767484 , DOI 10.1002/anie.201203459 , Abstract

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18524_2luj.nef
Input source #2: Coordindates	2luj.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	Error

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)
1:1:DT:O3'	1:2:IGU:P	unknown	unknown	n/a
1:2:IGU:O3'	1:3:IGU:P	unknown	unknown	n/a
1:3:IGU:O3'	1:4:IGU:P	unknown	unknown	n/a
1:4:IGU:O3'	1:5:IGU:P	unknown	unknown	n/a
1:5:IGU:O3'	1:6:DT:P	unknown	unknown	n/a
2:1:DT:O3'	2:2:IGU:P	unknown	unknown	n/a
2:2:IGU:O3'	2:3:IGU:P	unknown	unknown	n/a
2:3:IGU:O3'	2:4:IGU:P	unknown	unknown	n/a
2:4:IGU:O3'	2:5:IGU:P	unknown	unknown	n/a
2:5:IGU:O3'	2:6:DT:P	unknown	unknown	n/a
3:1:DT:O3'	3:2:IGU:P	unknown	unknown	n/a
3:2:IGU:O3'	3:3:IGU:P	unknown	unknown	n/a
3:3:IGU:O3'	3:4:IGU:P	unknown	unknown	n/a
3:4:IGU:O3'	3:5:IGU:P	unknown	unknown	n/a
3:5:IGU:O3'	3:6:DT:P	unknown	unknown	n/a
4:1:DT:O3'	4:2:IGU:P	unknown	unknown	n/a
4:2:IGU:O3'	4:3:IGU:P	unknown	unknown	n/a
4:3:IGU:O3'	4:4:IGU:P	unknown	unknown	n/a
4:4:IGU:O3'	4:5:IGU:P	unknown	unknown	n/a
4:5:IGU:O3'	4:6:DT:P	unknown	unknown	n/a
5:1:DT:O3'	5:2:IGU:P	unknown	unknown	n/a
5:2:IGU:O3'	5:3:IGU:P	unknown	unknown	n/a
5:3:IGU:O3'	5:4:IGU:P	unknown	unknown	n/a
5:4:IGU:O3'	5:5:IGU:P	unknown	unknown	n/a
5:5:IGU:O3'	5:6:DT:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	12	.	Not matched with CCD	None
A	10	.	Not matched with CCD	None
A	19	.	Not matched with CCD	None
A	28	.	Not matched with CCD	None
A	8	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
A	9	.	Not matched with CCD	None
A	7	.	Not matched with CCD	None
A	16	.	Not matched with CCD	Assigned chemical shifts, Distance restraints, Torsion angle restraints
A	14	.	Not matched with CCD	None
A	23	.	Not matched with CCD	None
A	13	.	Not matched with CCD	None
A	11	.	Not matched with CCD	None
A	20	.	Not matched with CCD	None
A	21	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
A	18	.	Not matched with CCD	None
A	17	.	Not matched with CCD	None
A	15	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
A	2	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
A	3	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints
A	4	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
A	5	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
A	24	.	Not matched with CCD	None
A	26	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
A	27	.	Not matched with CCD	None
A	29	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
B	15	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	Distance restraints
B	27	.	Not matched with CCD	None
B	8	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	Assigned chemical shifts, Distance restraints, Torsion angle restraints
B	23	.	Not matched with CCD	None
B	16	.	Not matched with CCD	None
B	11	.	Not matched with CCD	None
B	13	.	Not matched with CCD	None
B	7	.	Not matched with CCD	None
B	14	.	Not matched with CCD	None
B	19	.	Not matched with CCD	None
B	26	.	Not matched with CCD	None
B	20	.	Not matched with CCD	None
B	22	.	Not matched with CCD	None
B	21	.	Not matched with CCD	None
B	9	.	Not matched with CCD	None
B	10	.	Not matched with CCD	None
B	12	.	Not matched with CCD	None
B	17	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
B	2	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
B	3	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
B	4	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
B	5	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
B	18	.	Not matched with CCD	None
B	24	.	Not matched with CCD	None
B	28	.	Not matched with CCD	None
B	29	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	Assigned chemical shifts, Distance restraints, Torsion angle restraints
C	19	.	Not matched with CCD	None
C	28	.	Not matched with CCD	None
C	26	.	Not matched with CCD	None
C	23	.	Not matched with CCD	None
C	10	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
C	11	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
C	20	.	Not matched with CCD	None
C	14	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
C	15	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
C	16	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
C	17	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
C	21	.	Not matched with CCD	None
C	22	.	Not matched with CCD	None
C	24	.	Not matched with CCD	None
C	27	.	Not matched with CCD	None
C	29	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
D	13	.	Not matched with CCD	None
D	18	.	Not matched with CCD	None
D	9	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
D	14	.	Not matched with CCD	None
D	11	.	Not matched with CCD	None
D	17	.	Not matched with CCD	None
D	15	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
D	16	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
D	10	.	Not matched with CCD	None
D	20	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
D	21	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
D	22	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
D	23	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
E	16	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	Assigned chemical shifts, Distance restraints, Torsion angle restraints
E	21	.	Not matched with CCD	None
E	15	.	Not matched with CCD	None
E	23	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	None
E	26	.	Not matched with CCD	None
E	20	.	Not matched with CCD	None
E	25	.	Not matched with CCD	None
E	19	.	Not matched with CCD	None
E	13	.	Not matched with CCD	None
E	24	.	Not matched with CCD	None
E	12	.	Not matched with CCD	None
E	29	.	Not matched with CCD	None
E	14	0UH	2'-deoxy-2-oxoadenosine 5'-(dihydrogen phosphate)	Assigned chemical shifts, Distance restraints, Torsion angle restraints
E	17	.	Not matched with CCD	None
E	28	.	Not matched with CCD	None
E	22	.	Not matched with CCD	None
E	27	.	Not matched with CCD	None
E	7	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
E	8	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
E	9	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	None
E	10	IGU	2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE	Distance restraints

Sequence alignments

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

----------20--10-------------
X.X..............XTXXXXT..T.X
                  ||||||     
..................TXXXXT     
------------------------

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

-------- --     
..X...XX-TT     
          |     
-.-.-.-.-.-X-X-T
 - - - - - - - -

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

----20--------------1030
X..X..T......X....XXXXTT
                  ||||| 
.................TXXXXT 
-----------------------

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

----------20--10-------------
X.X..............XTXXXXT..T.X
                  ||||||     
..................TXXXXT     
------------------------

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

----------20--10-------------
X.X..............XTXXXXT..T.X
                  ||||||     
..................TXXXXT     
------------------------

Content subtype: combined_18524_2luj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	Warning	25		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	436		13.8 (chain: A, length: 29), 10.3 (chain: B, length: 29), 16.7 (chain: E, length: 24), 15.0 (chain: C, length: 20), 18.8 (chain: D, length: 16)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	Error	855 (1)	noe	13.8 (chain: A, length: 29), 10.3 (chain: B, length: 29), 16.7 (chain: E, length: 24), 15.0 (chain: C, length: 20), 18.8 (chain: D, length: 16)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	40 (1)	hbond	6.9 (chain: B, length: 29), 8.3 (chain: E, length: 24)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	Error	185 (185)	.	13.8 (chain: A, length: 29), 10.3 (chain: B, length: 29), 16.7 (chain: E, length: 24), 15.0 (chain: C, length: 20), 18.8 (chain: D, length: 16)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 13.8%
  - Entity_assembly_ID: B, Chain length: 29, Sequence coverage: 10.3%
  - Entity_assembly_ID: E, Chain length: 24, Sequence coverage: 16.7%
  - Entity_assembly_ID: C, Chain length: 20, Sequence coverage: 15.0%
  - Entity_assembly_ID: D, Chain length: 16, Sequence coverage: 18.8%
- Total number of assignments
  - ¹H chemical shifts: 305
  - ¹³C chemical shifts: 131
- Completeness of assignments
- Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: Warning

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 13.8%
  - Entity_assembly_ID: B, Chain length: 29, Sequence coverage: 10.3%
  - Entity_assembly_ID: E, Chain length: 24, Sequence coverage: 16.7%
  - Entity_assembly_ID: C, Chain length: 20, Sequence coverage: 15.0%
  - Entity_assembly_ID: D, Chain length: 16, Sequence coverage: 18.8%
- Total number of restraints: 855
- Weight of restraints: 1.0 (855)
- Potential type of restraints: square-well-parabolic (855)
- Range of distance target values: 2.0, 6.1 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 29, Sequence coverage: 6.9%
    - Entity_assembly_ID: E, Chain length: 24, Sequence coverage: 8.3%
  - Total number of restraints: 40
  - Weight of restraints: 1.0 (40)
  - Potential type of restraints: square-well-parabolic (40)
  - Range of distance target values: 2.7, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
    - Chain_ID: D
    - Chain_ID: E
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: Error
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 13.8%
  - Entity_assembly_ID: B, Chain length: 29, Sequence coverage: 10.3%
  - Entity_assembly_ID: E, Chain length: 24, Sequence coverage: 16.7%
  - Entity_assembly_ID: C, Chain length: 20, Sequence coverage: 15.0%
  - Entity_assembly_ID: D, Chain length: 16, Sequence coverage: 18.8%
- Total number of restraints: 185
- Total number of restraints per polymer type: 185
- Weight of restraints: 1.0 (185)
- Potential type of restraints: square-well-parabolic (185)
- Dihedral angle restraints per residue

Keywords isoguanine, parallel-stranded, pentaplex

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Found 1 Document (0.565 seconds)

BMRB: 18524

Sample #1

Sample #2

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail