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Found 1 Document (0.39 seconds)

BMRB: 18699

2LXV

DIMERIC PIL-E G-QUADRUPLEX DNA FROM NEISSERIA GONORRHOEAE, N STRUCTURES

Authors

Kuryavyi, V., Patel, D.J.

Assembly

DIMERIC PIL-E G-QUADRUPLEX DNA

Entity

1. DIMERIC PIL-E G-QUADRUPLEX DNA (polymer, Thiol state: not present), 16 monomers, 5185.255 × 2 Da Detail

GGGTGGGTTG GGTGGG

Total weight

10370.51 Da

Max. entity weight

5185.255 Da

Source organism

Neisseria gonorrhoeae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.1 %, Completeness (bb): 84.8 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	85.1 % (126 of 148)	85.1 % (126 of 148)
Suger, PO4	84.8 % (95 of 112)	84.8 % (95 of 112)
Nucleobase	86.1 % (31 of 36)	86.1 % (31 of 36)
Aromatic	84.4 % (27 of 32)	84.4 % (27 of 32)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. 5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP

GGGTGGGTTG GGTGGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi buffer, pH 6.8 at 25deg C

#	Name	Isotope labeling	Concentration
1	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	5 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi, pH 6.8

#	Name	Isotope labeling	Concentration
6	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	100 mM
9	sodium phosphate	natural abundance	5 mM

Release date

2012-11-01

Citation

RecA-binding pilE G4 sequence essential for pilin antigenic variation forms monomeric and 5' end-stacked dimeric parallel G-quadruplexes
Kuryavyi, V., Cahoon, L.A., Seifert, H., Patel, D.J.
Structure (2012), 20, 2090-2102, PubMed 23085077 , DOI 10.1016/j.str.2012.09.013 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18690 released on 2012-11-01
Title MOMERIC PIL-E G-QUADRUPLEX DNA FROM NEISSERIA GONORRHOEAE

Experiments performed 10 experiments Detail

1 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi buffer, pH 6.8 at 25deg C

#	Name	Isotope labeling	Concentration
1	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	5 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

2 1H-15N JRHMQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi buffer, pH 6.8 at 25deg C

#	Name	Isotope labeling	Concentration
1	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	5 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

3 1H-15N HMBC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi buffer, pH 6.8 at 25deg C

#	Name	Isotope labeling	Concentration
1	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	5 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

4 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi buffer, pH 6.8 at 25deg C

#	Name	Isotope labeling	Concentration
1	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	5 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

5 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi, pH 6.8

#	Name	Isotope labeling	Concentration
6	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	100 mM
9	sodium phosphate	natural abundance	5 mM

6 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi, pH 6.8

#	Name	Isotope labeling	Concentration
6	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	100 mM
9	sodium phosphate	natural abundance	5 mM

7 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi, pH 6.8

#	Name	Isotope labeling	Concentration
6	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	100 mM
9	sodium phosphate	natural abundance	5 mM

8 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi buffer, pH 6.8 at 25deg C

#	Name	Isotope labeling	Concentration
1	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	5 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

9 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi, pH 6.8

#	Name	Isotope labeling	Concentration
6	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	100 mM
9	sodium phosphate	natural abundance	5 mM

10 1H-31P COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 100 mM NaCl, 5mM NaPi, pH 6.8

#	Name	Isotope labeling	Concentration
6	di_PIL-E	natural abundance	0.3 ~ 3.5 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	100 mM
9	sodium phosphate	natural abundance	5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18699_2lxv.nef
Input source #2: Coordindates	2lxv.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------
GGGTGGGTTGGGTGGG
||||||||||||||||
GGGTGGGTTGGGTGGG

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

--------10------
GGGTGGGTTGGGTGGG
||||||||||||||||
GGGTGGGTTGGGTGGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	16	0	0	100.0
B	B	16	0	0	100.0

Content subtype: combined_18699_2lxv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	126		100.0 (chain: A, length: 16)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	294 (1)	noe	100.0 (chain: B, length: 16)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 126
- 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	148	126	85.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	112	95	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	31	86.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 100.0%
- Total number of restraints: 282
- Weight of restraints: 1.0 (282)
- Potential type of restraints: square-well-parabolic (282)
- Range of distance target values: 2.07, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
- Distance restraints on contact map

Keywords 5'-END STACKED DIMER, ALL-PARALLEL QUADRUPLEX, G-TETRAD, PILIN ANTIGE

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Found 1 Document (0.39 seconds)

BMRB: 18699

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail