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BMRB: 25582

2N21

structure of a protein

Authors

heddi, B., Cheong, V.V.V., Martadinata, H., Phan, A.A.T.

Assembly

Protein and DNA complex

Entity

1. Protein and DNA complex, entity 1 (polymer, Thiol state: not present), 20 monomers, 2354.752 Da Detail

SMHPGHLKGR EIGMWYAKKQ

2. DNA (polymer), 18 monomers, 5793.640 Da Detail

TTGGGTGGGT GGGTGGGT

Total weight

8148.392 Da

Max. entity weight

5793.64 Da

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing, distance geometry, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 47.4 %, Completeness: 47.1 %, Completeness (bb): 37.7 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	47.1 % (197 of 418)	35.4 % (107 of 302)	80.0 % (76 of 95)	66.7 % (14 of 21)
Backbone	37.7 % (92 of 244)	20.2 % (34 of 168)	77.2 % (44 of 57)	73.7 % (14 of 19)
Sidechain	62.3 % (119 of 191)	54.5 % (73 of 134)	83.6 % (46 of 55)	0.0 % (0 of 2)
Aromatic	32.8 % (21 of 64)	22.0 % (11 of 50)	76.9 % (10 of 13)	0.0 % (0 of 1)
Methyl	62.5 % (10 of 16)	45.5 % (5 of 11)	100.0 % (5 of 5)

1. entity 1

SMHPGHLKGR EIGMWYAKKQ

2. DNA

TTGGGTGGGT GGGTGGGT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2N21, Strand ID: A Detail

Release date

2015-07-26

Citation

Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex
Heddi, B., Cheong, V.V.V., Martadinata, H., Phan, A.A.T.
Proc. Natl. Acad. Sci. U. S. A. (2015), 112, 9608-9613, PubMed 26195789 , DOI 10.1073/pnas.1422605112 , Abstract

Related entities 1. Protein and DNA complex, entity 1, : 4 entities Detail

Related entities 2. DNA, : 2 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aliphatic

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 2D 1H-13C HSQC aromatic

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 2D 1H-1H NOESY

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D HNCO

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D CBCA(CO)NH

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D HNCACB

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 3D H(CCO)NH

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

10 3D HCCH-TOCSY

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

11 3D HNHA

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

12 3D 1H-13C NOESY

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

13 3D 1H-15N NOESY

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

14 3D 1H-13C NOESY aromatic

Instrument

Bruker AMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 (±11) K, pH 6.65 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		0.1 ~ 1.0 mM
2	DNA (5'-D(TPTPGPGPGPTPGPGPGPTPGPGPGPTPGPGPGPT)-3')	natural abundance		0.1 ~ 1.0 mM
3	potassium chloride	natural abundance		10.0 ~ 70.0 mM
4	potassium phosphate	natural abundance		10.0 ~ 20.0 mM
5	entity_1	natural abundance		0.1 ~ 1.0 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25582_2n21.nef
Input source #2: Coordindates	2n21.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--------20
SMHPGHLKGREIGMWYAKKQ
||||||||||||||||||||
SMHPGHLKGREIGMWYAKKQ

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

--------10--------
TTGGGTGGGTGGGTGGGT
||||||||||||||||||
TTGGGTGGGTGGGTGGGT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	20	0	0	100.0
B	B	18	0	0	100.0

Content subtype: combined_25582_2n21.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	197		90.0 (chain: A, length: 20)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	473 (1)	noe	90.0 (chain: A, length: 20), 100.0 (chain: B, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	16 (1)	undefined	77.8 (chain: B, length: 18)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	12 (12)	.	66.7 (chain: B, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 90.0%
- Total number of assignments
  - ¹H chemical shifts: 107
  - ¹³C chemical shifts: 76
  - ¹⁵N chemical shifts: 14
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 90.0%
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 467
- Weight of restraints: 1.0 (467)
- Potential type of restraints: square-well-parabolic (467)
- Range of distance target values: 2.0, 5.75 (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: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 77.8%
  - Total number of restraints: 16
  - Weight of restraints: 1.0 (16)
  - Potential type of restraints: square-well-parabolic (16)
  - Range of distance target values: 42.25, 42.25 (Å)
  - Distance restraints per residue
    - Chain_ID: A
      None
    - Chain_ID: B
  - 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: B, Chain length: 18, Sequence coverage: 66.7%
- Total number of restraints: 12
- Total number of restraints per polymer type: 12
- Weight of restraints: 1.0 (12)
- Potential type of restraints: square-well-parabolic (12)
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords protein