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Found 1 Document (0.687 seconds)

BMRB: 18951

2M3A

NMR solution structure of a MYB-like DNA binding domain of KNL-2 from C. Elegans

Authors

Osborne, M.J., Borden, K.LB.

Assembly

MYB-like DNA binding domain of KNL-2 from C. Elegans

Entity

1. MYB-like DNA binding domain of KNL-2 from C. Elegans (polymer, Thiol state: not present), 134 monomers, 15187.73 Da Detail

GPLGSVAKKI TWRKQDLDRL KRVIALKKPS ASDADWTEVL RLLAKEGVVE PEVVRQIAIT RLKWVEPGPL GSVAKKITWR KQDLDRLKRV IALKKPSASD ADWTEVLRLL AKEGVVEPEV VRQIAITRLK WVEP

Formula weight

15187.73 Da

Source organism

Caenorhabditis elegans

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 40.3 %, Completeness: 32.8 %, Completeness (bb): 33.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	32.8 % (535 of 1632)	33.7 % (289 of 858)	30.3 % (193 of 638)	39.0 % (53 of 136)
Backbone	33.1 % (261 of 788)	36.1 % (96 of 266)	29.0 % (115 of 396)	39.7 % (50 of 126)
Sidechain	33.2 % (323 of 972)	32.6 % (193 of 592)	34.3 % (127 of 370)	30.0 % (3 of 10)
Aromatic	19.4 % (14 of 72)	16.7 % (6 of 36)	20.0 % (6 of 30)	33.3 % (2 of 6)
Methyl	34.7 % (68 of 196)	34.7 % (34 of 98)	34.7 % (34 of 98)

1. KNL2

GPLGSVAKKI TWRKQDLDRL KRVIALKKPS ASDADWTEVL RLLAKEGVVE PEVVRQIAIT RLKWVEPGPL GSVAKKITWR KQDLDRLKRV IALKKPSASD ADWTEVLRLL AKEGVVEPEV VRQIAITRLK WVEP

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	KNL2	[U-99% 13C; U-99% 15N]	0.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	2 mM
5	sodium azide	natural abundance	0.02 %
6	Magnesium Sulphate	natural abundance	5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	KNL2	[U-99% 13C; U-99% 15N]	0.2 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	2 mM
11	sodium azide	natural abundance	0.02 %
12	Magnesium Sulphate	natural abundance	5 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2M3A, Strand ID: A Detail

Release date

2014-03-30

Citation

Centromere epigenome stability is mediated by structural recognition by the Centromere Licensing Complex
Padeganeh, A., De Rop, V., Dorn, J.F., Osborne, M.J., Boisvert, J., Ryan, J., Moevus, C., Borden, K.LB., Maddox, A.S., Maddox, P.S.
Science

Related entities 1. MYB-like DNA binding domain of KNL-2 from C. Elegans, : 1 entities Detail

Experiments performed 5 experiments Detail

1 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	KNL2	[U-99% 13C; U-99% 15N]	0.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	2 mM
5	sodium azide	natural abundance	0.02 %
6	Magnesium Sulphate	natural abundance	5 mM

2 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	KNL2	[U-99% 13C; U-99% 15N]	0.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	2 mM
5	sodium azide	natural abundance	0.02 %
6	Magnesium Sulphate	natural abundance	5 mM

3 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	KNL2	[U-99% 13C; U-99% 15N]	0.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	2 mM
5	sodium azide	natural abundance	0.02 %
6	Magnesium Sulphate	natural abundance	5 mM

4 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	KNL2	[U-99% 13C; U-99% 15N]	0.2 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	2 mM
11	sodium azide	natural abundance	0.02 %
12	Magnesium Sulphate	natural abundance	5 mM

5 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	KNL2	[U-99% 13C; U-99% 15N]	0.2 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	2 mM
11	sodium azide	natural abundance	0.02 %
12	Magnesium Sulphate	natural abundance	5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18951_2m3a.nef
Input source #2: Coordindates	2m3a.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--------30--------40--------50--------60-------
GPLGSVAKKITWRKQDLDRLKRVIALKKPSASDADWTEVLRLLAKEGVVEPEVVRQIAITRLKWVEP
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSVAKKITWRKQDLDRLKRVIALKKPSASDADWTEVLRLLAKEGVVEPEVVRQIAITRLKWVEP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	67	0	0	100.0

Content subtype: combined_18951_2m3a.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	506		70.1 (chain: A, length: 67)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1762 (1)	noe	95.5 (chain: A, length: 67)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 70.1%
- Total number of assignments
  - ¹H chemical shifts: 289
  - ¹³C chemical shifts: 170
  - ¹⁵N chemical shifts: 47
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	429	289	67.4
¹³C chemical shifts	319	170	53.3
¹⁵N chemical shifts	74	47	63.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	133	92	69.2
¹³C chemical shifts	134	47	35.1
¹⁵N chemical shifts	63	44	69.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	296	197	66.6
¹³C chemical shifts	185	123	66.5
¹⁵N chemical shifts	11	3	27.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	31	63.3
¹³C chemical shifts	49	31	63.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	12	66.7
¹³C chemical shifts	15	10	66.7
¹⁵N chemical shifts	3	2	66.7

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 95.5%
- Total number of restraints: 1755
- Weight of restraints: 1.0 (1755)
- Potential type of restraints: upper-bound-parabolic (1755)
- Range of distance target values: 2.77, 6.97 (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

Keywords KNL2

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Found 1 Document (0.687 seconds)

BMRB: 18951

Sample #1

Sample #2

Related entities 1. MYB-like DNA binding domain of KNL-2 from C. Elegans, : 1 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail