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BMRB: 19707

2MJ6

Solution structure of the extracellular sensor domain of DraK histidine kinase

Authors

Yeo, K., Cheong, H.

Assembly

extracellular sensor domain of DraK histidine kinase

Entity

1. extracellular sensor domain of DraK histidine kinase (polymer, Thiol state: not present), 90 monomers, 9749.702 Da Detail

GSETRTISST AQERVDLEAV RLASIVDSRL IGTGSVDEDF LREQIRDARY AVIRIPGQPV VEVGTKPTGD VLQGRATGEE GETVLVEEPR

Formula weight

9749.702 Da

Source organism

Streptomyces coelicolor

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.0 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.0 % (940 of 979)	96.4 % (489 of 507)	94.8 % (362 of 382)	98.9 % (89 of 90)
Backbone	97.6 % (519 of 532)	97.3 % (180 of 185)	97.3 % (254 of 261)	98.8 % (85 of 86)
Sidechain	94.9 % (501 of 528)	96.0 % (309 of 322)	93.1 % (188 of 202)	100.0 % (4 of 4)
Aromatic	44.4 % (8 of 18)	88.9 % (8 of 9)	0.0 % (0 of 9)
Methyl	97.5 % (117 of 120)	100.0 % (60 of 60)	95.0 % (57 of 60)

1. DraK

GSETRTISST AQERVDLEAV RLASIVDSRL IGTGSVDEDF LREQIRDARY AVIRIPGQPV VEVGTKPTGD VLQGRATGEE GETVLVEEPR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

LACS Plot; CA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.08 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MJ6, Strand ID: A Detail

Release date

2014-09-15

Citation

Mechanism of the pH-induced conformational change in the sensor domain of the DraK Histidine kinase via the E83, E105, and E107 residues
Yeo, K., Hong, Y., Jee, J., Lee, J., Kim, H., Park, J., Kim, E., Hwang, E., Kim, S., Lee, E., Kwon, O., Cheong, H.
PLoS One (2014), 9, e107168-e107168, PubMed 25203403 , DOI 10.1371/journal.pone.0107168 , Abstract

Related entities 1. extracellular sensor domain of DraK histidine kinase, : 1 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

2 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

3 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

5 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	DraK	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	sodium acetate	natural abundance		10 mM
5	NaCl	natural abundance		50 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_19707_2mj6.nef
Input source #2: Coordindates	2mj6.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--------70--------80--------90
GSETRTISSTAQERVDLEAVRLASIVDSRLIGTGSVDEDFLREQIRDARYAVIRIPGQPVVEVGTKPTGDVLQGRATGEEGETVLVEEPR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSETRTISSTAQERVDLEAVRLASIVDSRLIGTGSVDEDFLREQIRDARYAVIRIPGQPVVEVGTKPTGDVLQGRATGEEGETVLVEEPR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	90	0	0	100.0

Content subtype: combined_19707_2mj6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	953		100.0 (chain: A, length: 90)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2431 (1)	noe	98.9 (chain: A, length: 90)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_3	Warning	84 (83)	.	91.1 (chain: A, length: 90)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 499
  - ¹³C chemical shifts: 361
  - ¹⁵N chemical shifts: 93
- 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: 90, Sequence coverage: 98.9%
- Total number of restraints: 2431
- Weight of restraints: 1.0 (2431)
- Potential type of restraints: upper-bound-parabolic (2431)
- Range of distance target values: 2.5, 5.7 (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

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 91.1%
- Total number of restraints: 84
- Potential type of restraints: undefined (84)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords DraK