BMRBj - BMREntryMaster

Found 1 Document (0.368 seconds)

BMRB: 16225

2KH6

Solution Structure of cis-5R,6S-thymine glycol opposite complementary adenine in duplex DNA

Authors

Brown, K.L.

Assembly

5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3'

Entity

1. DNA (5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3') (polymer, Thiol state: not present), 12 monomers, 3812.397 Da Detail

GTGCGXGTTT GT

2. DNA (5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3') (polymer, Thiol state: not present), 12 monomers, 3672.370 Da Detail

ACAAACACGC AC

Total weight

7484.767 Da

Max. entity weight

3812.397 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 88.7 %, Completeness (bb): 90.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	88.7 % (219 of 247)	89.3 % (200 of 224)	82.6 % (19 of 23)
Suger, PO4	90.2 % (166 of 184)	91.3 % (147 of 161)	82.6 % (19 of 23)
Nucleobase	84.1 % (53 of 63)	84.1 % (53 of 63)
Aromatic	93.5 % (43 of 46)	93.5 % (43 of 46)
Methyl	100.0 % (5 of 5)	100.0 % (5 of 5)

1. DNA (5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3')

GTGCGXGTTT GT

2. DNA (5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3')

ACAAACACGC AC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	DNA_(5'-D(DGPDTPDGPDCPDGP(TG)PDGPDTPDTPDTPDGPDT)-3')		1 mM
2	DNA_(5'-D(DAPDCPDAPDAPDAPDCPDAPDCPDGPDCPDAPDC)-3')		1 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	10 uM
6	EDTA	natural abundance	50 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	DNA_(5'-D(DGPDTPDGPDCPDGP(TG)PDGPDTPDTPDTPDGPDT)-3')		1 mM
8	DNA_(5'-D(DAPDCPDAPDAPDAPDCPDAPDCPDGPDCPDAPDC)-3')		1 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	sodium azide	natural abundance	10 uM
12	EDTA	natural abundance	50 uM

Release date

2010-05-26

Citation

Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site
Brown, K.L., Roginskaya, M., Zou, Y., Altamirano, A., Basu, A.K., Stone, M.P.
Nucleic Acids Res. (2010), 38, 428-440, PubMed 19892827 , DOI 10.1093/nar/gkp844 , Abstract

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16225_2kh6.nef
Input source #2: Coordindates	2kh6.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)
1:5:DG:O3'	1:6:CTG:P	unknown	unknown	n/a
1:6:CTG:O3'	1:7:DG:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	6	CTG	(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--
GTGCGXGTTTGT
||||||||||||
GTGCGXGTTTGT

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

------20----
ACAAACACGCAC
||||||||||||
ACAAACACGCAC
--------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_16225_2kh6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	240		100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
1	Distance restraints	AMBER_distance_constraints_4	Warning	338 (1)	noe	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12)
2	Distance restraints	AMBER_distance_constraints_3	Warning	40 (1)	hbond	83.3 (chain: A, length: 12), 83.3 (chain: B, length: 12)
1	Dihedral angle restraints	AMBER_dihedral_2	OK	237 (237)	.	100.0 (chain: A, length: 12), 100.0 (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%
- Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 220
- ³¹P chemical shifts: 20

Completeness of assignments

Entity_assemble_ID: A

Comp_index_ID	Comp_ID
6	CTG

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	P	1.358
2	DT	P	1.453
3	DG	H22	6.353
3	DG	P	1.407
4	DC	P	1.289
5	DG	P	0.841
7	DG	H22	6.511
7	DG	P	1.436
8	DT	P	1.377
11	DG	H22	6.522
11	DG	P	1.355

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	93	87.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	67	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	26	89.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Entity_assemble_ID: B

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	DA	P	1.503
14	DC	P	1.012
15	DA	H62	6.042
15	DA	P	1.495
16	DA	H61	7.303
16	DA	H62	5.864
16	DA	P	1.434
17	DA	H62	5.702
17	DA	P	1.358
18	DC	P	1.543
19	DA	H62	6.146
19	DA	P	1.415
20	DC	P	1.209
21	DG	H22	6.3
21	DG	P	1.241
22	DC	P	1.635
23	DA	H61	8.014
23	DA	P	1.412

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	107	90.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	80	95.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	27	79.4

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	12	92.3

Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: AMBER_distance_constraints_4
- 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: 338
- Weight of restraints: 1.0 (338)
- Potential type of restraints: square-well-parabolic (338)
- Range of distance target values: 2.52, 7.03 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: AMBER_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: 40
  - Weight of restraints: 1.0 (40)
  - Potential type of restraints: square-well-parabolic (40)
  - Range of distance target values: 2.06, 3.2 (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: AMBER_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: 237
- Total number of restraints per polymer type: 237
- Weight of restraints: 1.0 (237)
- Potential type of restraints: square-well-parabolic (237)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords DNA, Thymine Glycol, NMR

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Found 1 Document (0.368 seconds)

BMRB: 16225

Sample #1

Sample #2

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail