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Found 1 Document (0.344 seconds)

BMRB: 19925

2MO7

Solution NMR structure of DNA dodecamer with A:C mismatch

Authors

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

Assembly

DNA dodecamer with A:C mismatch

Entity

1. DNA dodecamer with A:C mismatch (polymer, Thiol state: not present), 12 monomers, 3710.365 × 2 Da Detail

CGCAAATTCG CG

Total weight

7420.73 Da

Max. entity weight

3710.365 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 57.6 %, Completeness (bb): 56.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	57.6 % (68 of 118)	57.6 % (68 of 118)
Suger, PO4	56.0 % (47 of 84)	56.0 % (47 of 84)
Nucleobase	61.8 % (21 of 34)	61.8 % (21 of 34)
Aromatic	79.2 % (19 of 24)	79.2 % (19 of 24)
Methyl	100.0 % (2 of 2)	100.0 % (2 of 2)

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

CGCAAATTCG CG

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPGPCPAPAPAPTPTPCPGPCPG)-3')	natural abundance	100 mM
2	sodium phosphate	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	D2O	natural abundance	100 %
5	sodium azide	natural abundance	11 mM
6	EDTA	natural abundance	0.5 mM

Release date

2014-05-22

Citation

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

Experiments performed 1 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19925_2mo7.nef
Input source #2: Coordindates	2mo7.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10--
CGCAAATTCGCG
||||||||||||
CGCAAATTCGCG

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

------20----
CGCAAATTCGCG
||||||||||||
CGCAAATTCGCG
--------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_19925_2mo7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	68		100.0 (chain: A, length: 12)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	532 (1)	noe	100.0 (chain: A, length: 12), 100.0 (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)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	80 (80)	.	91.7 (chain: A, length: 12), 91.7 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 68
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	68	57.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	47	56.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	21	61.8

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	9	9	100.0

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: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 532
- Weight of restraints: 1.0 (532)
- Potential type of restraints: upper-bound-parabolic (532)
- Range of distance target values: 1.67, 6.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- 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: 80
- Total number of restraints per polymer type: 80
- Weight of restraints: 1.0 (80)
- Potential type of restraints: square-well-parabolic (80)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords DNA, dodecamer, mismatch

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Found 1 Document (0.344 seconds)

BMRB: 19925

Sample

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 5 contents Detail