BMRBj - BMREntryMaster

Found 1 Document (0.358 seconds)

BMRB: 19381

2MAY

Engineering G4: Towards effective incorporation of locked nucleic acid into G-quadruplexes

Authors

Li, Z., Lech, C., Adrian, M., Heddi, B., Phan, A.

Assembly

DNA/RNA (5'-D(*TP*TP*G)-R(P*(LG))-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')

Entity

1. DNA/RNA (5'-D(*TP*TP*G)-R(P*(LG))-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3') (polymer, Thiol state: not present), 24 monomers, 7682.863 Da Detail

TTGXGTTAGG GTTAGGGTTA GGGA

Formula weight

7682.863 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 74.9 %, Completeness (bb): 71.4 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	74.9 % (161 of 215)	74.9 % (161 of 215)
Suger, PO4	71.4 % (115 of 161)	71.4 % (115 of 161)
Nucleobase	85.2 % (46 of 54)	85.2 % (46 of 54)
Aromatic	82.6 % (38 of 46)	82.6 % (38 of 46)
Methyl	100.0 % (8 of 8)	100.0 % (8 of 8)

1. DNA (5'-D(*TP*TP*GP*LGP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')

TTGXGTTAGG GTTAGGGTTA GGGA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(TPTPGPLGPGPTPTPAPGPGPGPTPTPAPGPGPGPTPTPAPGPGPGPA)-3')	natural abundance	1.5 mM
2	DSS	natural abundance	20 uM
3	potassium phosphate	natural abundance	20 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	DNA (5'-D(TPTPGPLGPGPTPTPAPGPGPGPTPTPAPGPGPGPTPTPAPGPGPGPA)-3')	natural abundance	1.5 mM
7	DSS	natural abundance	20 uM
8	potassium phosphate	natural abundance	20 mM
9	D2O	natural abundance	100 %

Release date

2015-02-01

Citation

Engineering G4: Towards effective incorporation of locked nucleic acid into G-quadruplexes
Li, Z., Lech, C., Adrian, M., Heddi, B., Phan, A.
Not known

Related entities 1. DNA/RNA (5'-D(TPTPG)-R(P(LG))-D(PGPTPTPAPGPGPGPTPTPAPGPGPGPTPTPAPGPGPGPA)-3'), : 1 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19381_2may.nef
Input source #2: Coordindates	2may.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)
1:3:DG:O3'	1:4:LCG:P	unknown	unknown	n/a
1:4:LCG:O3'	1:5:DG:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	4	LCG	[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--------10--------20----
TTGXGTTAGGGTTAGGGTTAGGGA
||||||||||||||||||||||||
TTGXGTTAGGGTTAGGGTTAGGGA

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_19381_2may.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	170		100.0 (chain: A, length: 24)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	519 (1)	noe	100.0 (chain: A, length: 24)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	56 (1)	hbond	66.7 (chain: A, length: 24)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	28 (28)	.	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: 170
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
4	LCG

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	215	161	74.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	115	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	46	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	19	100.0

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: 100.0%
- Total number of restraints: 519
- Weight of restraints: 1.0 (519)
- Potential type of restraints: square-well-parabolic (519)
- Range of distance target values: 2.6, 6.05 (Å)
- Histogram of 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: 66.7%
  - Total number of restraints: 56
  - Weight of restraints: 1.0 (56)
  - Potential type of restraints: square-well-parabolic (56)
  - Range of distance target values: 1.95, 2.99 (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: 28
- Total number of restraints per polymer type: 28
- Weight of restraints: 1.0 (28)
- Potential type of restraints: square-well-parabolic (28)
- Dihedral angle restraints per residue

Keywords Backbone, G-quadruplex, LNA modification, loop

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Found 1 Document (0.358 seconds)

BMRB: 19381

Sample #1

Sample #2

Related entities 1. DNA/RNA (5'-D(TPTPG)-R(P(LG))-D(PGPTPTPAPGPGPGPTPTPAPGPGPGPTPTPAPGPGPGPA)-3'), : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail

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 (0.358 seconds)

BMRB: 19381

Sample #1

Sample #2

Related entities 1. DNA/RNA (5'-D(*TP*TP*G)-R(P*(LG))-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail

Related entities 1. DNA/RNA (5'-D(TPTPG)-R(P(LG))-D(PGPTPTPAPGPGPGPTPTPAPGPGPGPTPTPAPGPGPGPA)-3'), : 1 entities Detail