BMRBj - BMREntryMaster

Found 1 Document (0.225 seconds)

BMRB: 34378

Structure of kiteplatinated dsDNA

Authors

Margiotta, N., Papadia, P., Kubicek, K., Krejcikova, M., Gkionis, K., Sponer, J.

Assembly

Kiteplatinated DNA oligomer

Entity

1. Kiteplatinated DNA oligomer, entity 1 (polymer, Thiol state: not present), 12 monomers, 3622.291 Da Detail

CCTCAGGCCT CC

2. Kiteplatinated DNA oligomer, entity 2 (polymer, Thiol state: not present), 12 monomers, 3831.425 Da Detail

GGAGGCCTGA GG

3. Kiteplatinated DNA oligomer, entity LN8 (non-polymer), 380.173 Da

Total weight

7833.8887 Da

Max. entity weight

3831.425 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 81.9 %, Completeness (bb): 88.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	81.9 % (194 of 237)	81.9 % (194 of 237)
Suger, PO4	88.1 % (148 of 168)	88.1 % (148 of 168)
Nucleobase	66.7 % (46 of 69)	66.7 % (46 of 69)
Aromatic	89.6 % (43 of 48)	89.6 % (43 of 48)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. entity 1

CCTCAGGCCT CC

2. entity 2

GGAGGCCTGA GG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM NA- kiteplatin, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	entity_2	natural abundance	1 mM
3	kiteplatin	natural abundance	1 mM

Release date

2019-10-21

Citation

Structural characterization of kiteplatinated DNA
Krejcikova, M., Papadia, P., Gkionis, K., Plats, J., Petruzzella, E., Savino, S., Hoeschelle, J.D., Natile, G., Sponer, J., Kubicek, K., Margiotta, N.

Experiments performed 7 experiments Detail

1 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 600 MHz QCI cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.1) K, pH 7.0 (±0.1), Details 1 mM NA- kiteplatin, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	entity_2	natural abundance	1 mM
3	kiteplatin	natural abundance	1 mM

2 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 950 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.1) K, pH 7.0 (±0.1), Details 1 mM NA- kiteplatin, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	entity_2	natural abundance	1 mM
3	kiteplatin	natural abundance	1 mM

3 2D DQF-COSY

Instrument

Bruker AVANCE III - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM NA- kiteplatin, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	entity_2	natural abundance	1 mM
3	kiteplatin	natural abundance	1 mM

4 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM NA- kiteplatin, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	entity_2	natural abundance	1 mM
3	kiteplatin	natural abundance	1 mM

5 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM NA- kiteplatin, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	entity_2	natural abundance	1 mM
3	kiteplatin	natural abundance	1 mM

6 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 950 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM NA- kiteplatin, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	entity_2	natural abundance	1 mM
3	kiteplatin	natural abundance	1 mM

7 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 (±0.1) K, pH 7.0 (±0.1), Details 1 mM NA- kiteplatin, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1 mM
2	entity_2	natural abundance	1 mM
3	kiteplatin	natural abundance	1 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34378_3.str
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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr34378_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	200		100.0 (chain: 1, length: 12), 100.0 (chain: 2, length: 12)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 200
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	95	76.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	71	84.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	24	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	113	99	87.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	77	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	22	75.9

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	11	100.0

Keywords DNA, kiteplatin

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 (0.225 seconds)

BMRB: 34378

Sample

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 5 contents Detail