BMRBj - BMREntryMaster

Found 1 Document (0.336 seconds)

BMRB: 19917

2MO2

Solution NMR structure of DNA dodecamer containing the 5-hydroxycytosine

Authors

Donahue, P.S., Szulik, M.W., Stone, M.P.

Assembly

DNA dodecamer containing the 5-hydroxycytosine

Entity

1. DNA dodecamer containing the 5-hydroxycytosine (polymer, Thiol state: not present), 12 monomers, 3742.364 × 2 Da Detail

CGCGAATTXG CG

Total weight

7484.728 Da

Max. entity weight

3742.364 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.7 %, Completeness: 57.9 %, Completeness (bb): 57.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	57.9 % (62 of 107)	57.9 % (62 of 107)
Suger, PO4	57.1 % (44 of 77)	57.1 % (44 of 77)
Nucleobase	60.0 % (18 of 30)	60.0 % (18 of 30)
Aromatic	72.7 % (16 of 22)	72.7 % (16 of 22)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

1. DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3')

CGCGAATTXG CG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPGPCPGPAPAPTPTP(OHC)PGPCPG)-3')	natural abundance	100 mM
2	D2O	natural abundance	10 %
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	11 mM
6	EDTA	natural abundance	0.05 mM
7	H2O	natural abundance	90 %

Release date

2014-05-22

Citation

Characterization of 5-hydroxycytosine in DNA
Szulik, M.
Not known

Experiments performed 2 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19917_2mo2.nef
Input source #2: Coordindates	2mo2.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:DT:O3'	1:9:5OC:P	unknown	unknown	n/a
2:8:DT:O3'	2:9:5OC:P	unknown	unknown	n/a
1:9:5OC:O3'	1:10:DG:P	unknown	unknown	n/a
2:9:5OC:O3'	2:10:DG:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	9	5OC	2'-deoxy-5-hydroxycytidine 5'-(dihydrogen phosphate)	Assigned chemical shifts, Coordinates
B	21	5OC	2'-deoxy-5-hydroxycytidine 5'-(dihydrogen phosphate)	Coordinates

Sequence alignments

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

--------10--
CGCGAATTXGCG
||||||||||||
CGCGAATTXGCG

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

------20----
CGCGAATTXGCG
||||||||||||
CGCGAATTXGCG
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	12	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_19917_2mo2.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	65		100.0 (chain: A, length: 12)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	416 (1)	noe	91.7 (chain: A, length: 12), 91.7 (chain: B, length: 12)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	42 (1)	hbond	83.3 (chain: A, length: 12), 83.3 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 65
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
9	5OC

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	62	57.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	44	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	18	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	8	8	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 91.7%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 91.7%
- Total number of restraints: 416
- Weight of restraints: 1.0 (416)
- Potential type of restraints: upper-bound-parabolic (416)
- Range of distance target values: 1.0, 5.2 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 83.3%
    - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 83.3%
  - Total number of restraints: 42
  - Weight of restraints: 1.0 (42)
  - Potential type of restraints: upper-bound-parabolic (42)
  - Range of distance target values: 1.71, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Keywords 5-hydroxycytosine, DNA

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 (0.336 seconds)

BMRB: 19917

Sample

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail