BMRBj - BMREntryMaster

Found 1 Document (0.332 seconds)

BMRB: 11528

2RT8

STRUCTURE OF METALLO-DNA IN SOLUTION

Authors

Yamaguchi, H., Sebera, J., Kondo, J., Oda, S., Komuro, T., Kawamura, T., Dairaku, T., Kondo, Y., Okamoto, I., Ono, A., Burda, J.V., Kojima, C., Sychrovsky, V., Tanaka, Y.

Assembly

METALLO-BASE-PAIRED DNA

Entity

1. 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' (polymer, Thiol state: not present), 10 monomers, 3074.937 Da Detail

CGCGTTGTCC

2. 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' (polymer, Thiol state: not present), 10 monomers, 3123.975 Da Detail

GGACTTCGCG

3. MERCURY (II) ION (non-polymer), 200.590 × 2 Da

Total weight

6600.0923 Da

Max. entity weight

3123.975 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	98.0 % (195 of 199)	98.0 % (195 of 199)
Suger, PO4	100.0 % (140 of 140)	100.0 % (140 of 140)
Nucleobase	93.2 % (55 of 59)	93.2 % (55 of 59)
Aromatic	90.0 % (36 of 40)	90.0 % (36 of 40)
Methyl	100.0 % (5 of 5)	100.0 % (5 of 5)

1. 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'

CGCGTTGTCC

2. 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'

GGACTTCGCG

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 2.0 MM DNA DUPLEX (10BP), 100 MM SODIUM PERCHLORATE, 4.0 MM MERCURY(II) PERCHLORATE-2

#	Name	Isotope labeling	Type	Concentration
1	5'-D(CPGPCPGPTPTPGPTPCPC)-3'	natural abundance	DNA	2.0 mM
2	5'-D(GPGPAPCPTPTPCPGPCPG)-3'	natural abundance	DNA	2.0 mM
3	Mercury(II) perchlorate	natural abundance		4.0 mM
4	Sodium perchlorate	natural abundance		100 mM
5	D2O	[U-100% 2H]	solvent	100 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 2.0 MM DNA DUPLEX (10BP), 100 MM SODIUM PERCHLORATE, 4.0 MM MERCURY(II) PERCHLORATE-2

#	Name	Isotope labeling	Type	Concentration
6	5'-D(CPGPCPGPTPTPGPTPCPC)-3'	natural abundance	DNA	2.0 mM
7	5'-D(GPGPAPCPTPTPCPGPCPG)-3'	natural abundance	DNA	2.0 mM
8	Mercury(II) perchlorate	natural abundance		4.0 mM
9	Sodium perchlorate	natural abundance		100 mM
10	H2O	natural abundance	solvent	95 %
11	D2O	[U-100% 2H]	solvent	5 %

Release date

2014-03-02

Citation

The structure of metallo-DNA with consecutive T-Hg(II)-T base-pairs explains positive entropy for the metallo-base-pair formation
Yamaguchi, H., Sebera, J., Kondo, J., Oda, S., Komuro, T., Kawamura, T., Dairaku, T., Kondo, Y., Okamoto, I., Ono, A., Burda, J.V., Kojima, C., Sychrovsky, V., Tanaka, Y.
Not known

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_11528_2rt8.nef
Input source #2: Coordindates	2rt8.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	Distance (Å)
A:6:DT:N3	D:null:HG:HG	2.039
B:5:DT:N3	D:null:HG:HG	2.039
A:5:DT:N3	C:null:HG:HG	2.044
B:6:DT:N3	C:null:HG:HG	2.044
A:5:DT:O4	C:null:HG:HG	2.987
B:6:DT:O4	C:null:HG:HG	2.995
A:6:DT:O4	D:null:HG:HG	3.011
B:5:DT:O4	D:null:HG:HG	3.018
A:6:DT:O2	D:null:HG:HG	3.054
B:5:DT:O2	D:null:HG:HG	3.055
B:6:DT:O2	C:null:HG:HG	3.083
A:5:DT:O2	C:null:HG:HG	3.101

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	HG	MERCURY (II) ION	None
C	2	HG	MERCURY (II) ION	None

Sequence alignments

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

--------10
CGCGTTGTCC
||||||||||
CGCGTTGTCC

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

--------20
GGACTTCGCG
||||||||||
GGACTTCGCG
--------10

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	10	0	0	100.0
B	B	10	0	0	100.0

Content subtype: combined_11528_2rt8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	12		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	210		100.0 (chain: A, length: 10), 100.0 (chain: B, length: 10)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	628 (1)	noe	100.0 (chain: A, length: 10), 100.0 (chain: B, length: 10)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	55 (1)	hbond	80.0 (chain: A, length: 10), 80.0 (chain: B, length: 10)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	57 (57)	.	100.0 (chain: A, length: 10), 90.0 (chain: B, length: 10)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 210
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DG	H21	8.47
2	DG	H22	6.99
4	DG	H21	8.33
4	DG	H22	7.22
7	DG	H22	6.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	99	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	70	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	29	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
11	DG	H21	8.38
11	DG	H22	6.51
12	DG	H21	8.07
12	DG	H22	6.84
13	DA	H61	8.21
13	DA	H62	6.59
18	DG	H21	8.34
18	DG	H22	6.91
20	DG	H21	7.25
20	DG	H22	6.95

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	96	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	70	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	26	92.9

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	6	6	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 628
- Weight of restraints: 1.0 (628)
- Potential type of restraints: square-well-parabolic (628)
- Range of distance target values: 1.86, 7.21 (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
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 80.0%
    - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 80.0%
  - Total number of restraints: 55
  - Weight of restraints: 1.0 (55)
  - Potential type of restraints: square-well-parabolic (55)
  - Range of distance target values: 1.9, 5.35 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
  - 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: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 90.0%
- Total number of restraints: 57
- Total number of restraints per polymer type: 57
- Weight of restraints: 1.0 (57)
- Potential type of restraints: square-well-parabolic (57)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

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Found 1 Document (0.332 seconds)

BMRB: 11528

Sample #1

Sample #2

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail