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BMRB: 15444

2JUH

solution structure of DNA binding domain of ngTRF1

Authors

Lee, W., Ko, S.

Assembly

DNA binding domain of NgTRF1 monomer

Entity

1. DNA binding domain of NgTRF1 monomer (polymer, Thiol state: all free), 121 monomers, 13883.62 Da Detail

PVNQKSKRSE LSQRRIRRPF SVAEVEALVE AVEHLGTGRW RDVKMRAFDN ADHRTYVDLK DKWKTLVHTA SIAPQQRRGE PVPQDLLDRV LAAHAYWSQQ QGKQHVEPLK ILDAKAQKVG A

Formula weight

13883.62 Da

Source organism

Nicotiana tabacum

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 69.9 %, Completeness (bb): 93.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	69.9 % (1010 of 1445)	61.5 % (469 of 762)	77.0 % (426 of 553)	88.5 % (115 of 130)
Backbone	93.3 % (666 of 714)	84.2 % (203 of 241)	98.0 % (351 of 358)	97.4 % (112 of 115)
Sidechain	54.0 % (457 of 847)	51.1 % (266 of 521)	60.5 % (188 of 311)	20.0 % (3 of 15)
Aromatic	14.1 % (13 of 92)	21.7 % (10 of 46)	0.0 % (0 of 43)	100.0 % (3 of 3)
Methyl	77.6 % (104 of 134)	79.1 % (53 of 67)	76.1 % (51 of 67)

1. NgTRF1

PVNQKSKRSE LSQRRIRRPF SVAEVEALVE AVEHLGTGRW RDVKMRAFDN ADHRTYVDLK DKWKTLVHTA SIAPQQRRGE PVPQDLLDRV LAAHAYWSQQ QGKQHVEPLK ILDAKAQKVG A

Show sample condition

Sample #1

Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

Sample #2

Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
6	NgTRF1	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	NaCl			100 mM
9	H2O			90 %
10	D2O			10 %

LACS Plot; CA

Referencing offset: 0.02 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.02 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.23 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JUH, Strand ID: A Detail

Release date

2008-08-26

Citation

Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins
Ko, S., Jun, S., Bae, H., Byun, J., Han, W., Park, H., Yang, S., Park, S., Jeon, Y., Cheong, C., Kim, W., Lee, W., Cho, H.
Nucleic Acids Res. (2008), 36, 2739-2755, PubMed 18367475 , DOI 10.1093/nar/gkn030 , Abstract

Related entities 1. DNA binding domain of NgTRF1 monomer, : 1 : 26 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

2 3D CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

3 3D HNCO

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

4 3D HNCACB

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

5 3D 1H-13C NOESY

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

6 3D HNCA

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

7 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

8 3D HBHA(CO)NH

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

9 3D 1H-13C NOESY

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

10 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz with Cryo-probe

Sample

State isotropic, Solvent system 25mM Sodium phosphate, 100mM NaCl, pH 7, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NgTRF1	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	NaCl			100 mM
4	H2O			90 %
5	D2O			10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15444_2juh.nef
Input source #2: Coordindates	2juh.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

-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660
PVNQKSKRSELSQRRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAYWSQQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PVNQKSKRSELSQRRIRRPFSVAEVEALVEAVEHLGTGRWRDVKMRAFDNADHRTYVDLKDKWKTLVHTASIAPQQRRGEPVPQDLLDRVLAAHAYWSQQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------670-------680-
QGKQHVEPLKILDAKAQKVGA
|||||||||||||||||||||
QGKQHVEPLKILDAKAQKVGA
-------110-------120-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	121	0	0	100.0

Content subtype: combined_15444_2juh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	987		100.0 (chain: A, length: 121)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1854 (1)	noe	70.2 (chain: A, length: 121)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	62 (1)	hbond	37.2 (chain: A, length: 121)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	546 (546)	.	80.2 (chain: A, length: 121)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 423
  - ¹H chemical shifts: 450
  - ¹⁵N chemical shifts: 114
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 70.2%
- Total number of restraints: 1854
- Weight of restraints: 1.0 (1854)
- Potential type of restraints: upper-bound-parabolic (1854)
- Range of distance target values: 2.29, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 37.2%
  - Total number of restraints: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: upper-bound-parabolic (62)
  - Range of distance target values: 2.3, 3.3 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 80.2%
- Total number of restraints: 546
- Total number of restraints per polymer type: 546
- Weight of restraints: 1.0 (546)
- Potential type of restraints: square-well-parabolic (546)
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A