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BMRB: 25142

2MSY

Solution structure of Hox homeodomain

Authors

Kim, H., Park, S., Han, J., Lee, B.

Assembly

Hox homeodomain

Entity

1. Hox homeodomain (polymer), 68 monomers, 8658.101 Da Detail

ANWIHARSTR KKRCPYTKYQ TLELEKEFLF NMYLTRDRRY EVARVLNLTE RQVKIWFQNR RMKMKKMN

Formula weight

8658.101 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 79.4 %, Completeness (bb): 94.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.4 % (720 of 907)	74.7 % (363 of 486)	82.8 % (285 of 344)	93.5 % (72 of 77)
Backbone	94.8 % (385 of 406)	94.1 % (127 of 135)	94.1 % (192 of 204)	98.5 % (66 of 67)
Sidechain	69.9 % (398 of 569)	67.2 % (236 of 351)	75.0 % (156 of 208)	60.0 % (6 of 10)
Aromatic	34.4 % (31 of 90)	40.0 % (18 of 45)	27.9 % (12 of 43)	50.0 % (1 of 2)
Methyl	91.7 % (55 of 60)	90.0 % (27 of 30)	93.3 % (28 of 30)

1. entity

ANWIHARSTR KKRCPYTKYQ TLELEKEFLF NMYLTRDRRY EVARVLNLTE RQVKIWFQNR RMKMKKMN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.24 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.24 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.7 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2015-09-13

Citation

Structural insight into the interaction between the Hox and HMGB1 and understanding of the HMGB1-enhancing effect of Hox-DNA binding
Kim, H., Park, S., Han, J., Pathak, C., Cheong, H., Lee, B.
Biochim. Biophys. Acta (2015), 1854, 449-459, PubMed 25707357 , DOI 10.1016/j.bbapap.2015.02.009 , Abstract

Related entities 1. Hox homeodomain, : 1 : 9 : 27 : 1 : 250 entities Detail

Interaction partners 1. Hox homeodomain, : 3 interactors Detail

More details for 3 interactors identified by 1 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 3D 1H-15N NOESY

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 3D 1H-13C NOESY

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D HNCO

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D 1H-15N TOCSY

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

9 3D HBHA(CO)NH

Instrument

Bruker DRX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	MES	[U-100% 13C; U-100% 15N]		1 mM
2	H2O	natural abundance		90 %
3	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_25142_2msy.nef
Input source #2: Coordindates	2msy.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--------
ANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	68	0	0	100.0

Content subtype: combined_25142_2msy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	719		98.5 (chain: A, length: 68)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	934 (1)	noe	91.2 (chain: A, length: 68)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	32 (1)	hbond	38.2 (chain: A, length: 68)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	100 (100)	.	77.9 (chain: A, length: 68)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 98.5%
- Total number of assignments
  - ¹H chemical shifts: 363
  - ¹³C chemical shifts: 285
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 91.2%
- Total number of restraints: 934
- Weight of restraints: 1.0 (934)
- Potential type of restraints: square-well-parabolic (934)
- Range of distance target values: 2.08, 3.69 (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: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 38.2%
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: square-well-parabolic (32)
  - Range of distance target values: 2.05, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: A, Chain length: 68, Sequence coverage: 77.9%
- Total number of restraints: 100
- Total number of restraints per polymer type: 100
- Weight of restraints: 1.0 (100)
- Potential type of restraints: square-well-parabolic (100)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords homeodomain, transcription factor