BMRBj - BMREntryMaster

Found 1 Document (0.371 seconds)

BMRB: 16834

2KAL

NMR structure of fully methylated GATC site

Authors

Bang, J., Bae, S., Park, C., Lee, J., Choi, B.

Assembly

5'-D(*DGP*DCP*DGP*DAP*DGP*(6MT)P*DTP*DCP*DTP*DGP*DCP*DG)-3'

Entity

1. DNA 1 (polymer, Thiol state: not present), 12 monomers, 3766.388 Da Detail

GCGAGATCTG CG

2. DNA 2 (polymer, Thiol state: not present), 12 monomers, 3686.340 Da Detail

CGCAGATCTC GC

Total weight

7452.728 Da

Max. entity weight

3766.388 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 54.7 %, Completeness (bb): 54.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	54.7 % (129 of 236)	54.7 % (129 of 236)
Suger, PO4	54.2 % (91 of 168)	54.2 % (91 of 168)
Nucleobase	55.9 % (38 of 68)	55.9 % (38 of 68)
Aromatic	70.8 % (34 of 48)	70.8 % (34 of 48)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. DNA 1

GCGAGATCTG CG

2. DNA 2

CGCAGATCTC GC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 287 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
2	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Temperature 287 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
6	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
7	D2O	natural abundance	100 %

Release date

2010-07-26

Citation

Structural and dynamics study of DNA dodecamer duplexes that contain un-, hemi-, or fully methylated GATC sites
Bang, J., Bae, S., Park, C., Lee, J., Choi, B.
J. Am. Chem. Soc. (2008), 130, 17688-17696, PubMed 19108701 , DOI 10.1021/ja8038272 , Abstract

Experiments performed 7 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 287 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
6	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
7	D2O	natural abundance	100 %

2 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 287 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
6	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
7	D2O	natural abundance	100 %

3 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 287 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
6	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
7	D2O	natural abundance	100 %

4 2D 1H-13C HSQC

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
6	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
7	D2O	natural abundance	100 %

5 2D 1H-13C HSQC

Instrument

Varian INOVA - 900 MHz

Sample

State anisotropic, Solvent system 100% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Concentration
5	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
6	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
7	D2O	natural abundance	100 %

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
2	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

7 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 308 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	DNA GCGAGATCTGCG	natural abundance	0.5 ~ 1.0 mM
2	DNA CGCAGATCTCGC	natural abundance	0.5 ~ 1.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16834_2kal.nef
Input source #2: Coordindates	2kal.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	Error

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)
1:5:DG:O3'	1:6:6MA:P	unknown	unknown	n/a
1:6:6MA:O3'	1:7:DT:P	unknown	unknown	n/a
2:5:DG:O3'	2:6:6MA:P	unknown	unknown	n/a
2:6:6MA:O3'	2:7:DT:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	6	6MA	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE	Distance restraints, Torsion angle restraints, RDC restraints, Coordinates
B	18	6MA	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE	Distance restraints, Torsion angle restraints, RDC restraints, Coordinates

Sequence alignments

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

--------10--
GCGAGXTCTGCG
||||||||||||
GCGAGXTCTGCG

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

------20----
CGCAGXTCTCGC
||||||||||||
CGCAGXTCTCGC
--------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_16834_2kal.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	Error	89		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	349 (1)	noe	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	32 (1)	hbond	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	114 (114)	.	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	22 (22)	.	58.3 (chain: A, length: 12), 50.0 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- 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: 348
- Weight of restraints: 1.0 (348)
- Potential type of restraints: square-well-parabolic (348)
- Range of distance target values: 1.9, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 12, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: square-well-parabolic (32)
  - Range of distance target values: 2.9, 2.95 (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: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- 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: 114
- Total number of restraints per polymer type: 114
- Weight of restraints: 1.0 (114)
- Potential type of restraints: square-well-parabolic (114)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 58.3%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 50.0%
- Total number of restraints: 22
- Potential type of restraints: undefined (22)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
    None

Keywords GATC, N6-methylated adenine

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Found 1 Document (0.371 seconds)

BMRB: 16834

Sample #1

Sample #2

Experiments performed 7 experiments Detail

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NMR combined restraints 6 contents Detail