BMRBj - BMREntryMaster

Found 1 Document (0.709 seconds)

BMRB: 16947

2KSD

Backbone structure of the membrane domain of E. coli histidine kinase receptor ArcB

Authors

Maslennikov, I., Klammt, C., Hwang, E., Kefala, G., Kwiatkowski, W., Jeon, Y., Choe, S.

Assembly

histidine kinase receptor ArcB

Entity

1. histidine kinase receptor ArcB (polymer, Thiol state: not present), 115 monomers, 13290.86 Da Detail

MKQIRLLAQY YVDLMMKLGL VRFSMLLALA LVVLAIVVQM AVTMVLHGQV ESIDVIRSIF FGLLITPWAV YFLSVVVEQL EESRQRLSRL VQKLEEMRER DLSLNVQLKD NIAQL

Formula weight

13290.86 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.3 %, Completeness: 67.0 %, Completeness (bb): 93.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.0 % (953 of 1423)	66.4 % (488 of 735)	63.3 % (356 of 562)	86.5 % (109 of 126)
Backbone	93.6 % (644 of 688)	92.2 % (214 of 232)	93.9 % (321 of 342)	95.6 % (109 of 114)
Sidechain	48.9 % (414 of 847)	54.5 % (274 of 503)	42.2 % (140 of 332)	0.0 % (0 of 12)
Aromatic	7.5 % (6 of 80)	10.0 % (4 of 40)	5.1 % (2 of 39)	0.0 % (0 of 1)
Methyl	38.4 % (76 of 198)	51.5 % (51 of 99)	25.3 % (25 of 99)

1. ArcB

MKQIRLLAQY YVDLMMKLGL VRFSMLLALA LVVLAIVVQM AVTMVLHGQV ESIDVIRSIF FGLLITPWAV YFLSVVVEQL EESRQRLSRL VQKLEEMRER DLSLNVQLKD NIAQL

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in E. coli

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	sodium acetate	natural abundance	20 mM
3	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	200 mM
4	sodium chloride	natural abundance	10 mM
5	Protein	[U-98% 13C; U-98% 15N]	0.5 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in CF system

#	Name	Isotope labeling	Concentration
8	DSS	natural abundance	0.5 mM
9	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	100 mM
10	Mes-BisTris	natural abundance	20 mM
11	Protein	[U-99% 13C; U-99% 15N]	0.3 mM
12	H2O	natural abundance	95 %
13	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	direct	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	direct	0.1013291

Referencing offset: 0.52 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	direct	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	direct	0.1013291

Referencing offset: 0.52 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	direct	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	direct	0.1013291

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	direct	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	direct	0.1013291

Referencing offset: 0.24 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2010-06-14

Citation

Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis
Maslennikov, I., Klammt, C., Hwang, E., Kefala, G., Okamura, M., Esquivies, L., Mors, K., Glaubitz, C., Kwiatkowski, W., Jeon, Y., Choe, S.
Proc. Natl. Acad. Sci. U. S. A. (2010), 107, 10902-10907, PubMed 20498088 , DOI 10.1073/pnas.1001656107 , Abstract

Related entities 1. histidine kinase receptor ArcB, : 1 : 3 : 2 entities Detail

Interaction partners 1. histidine kinase receptor ArcB, : 12 interactors Detail

More details for 12 interactors identified by 5 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in E. coli

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	sodium acetate	natural abundance	20 mM
3	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	200 mM
4	sodium chloride	natural abundance	10 mM
5	Protein	[U-98% 13C; U-98% 15N]	0.5 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in CF system

#	Name	Isotope labeling	Concentration
8	DSS	natural abundance	0.5 mM
9	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	100 mM
10	Mes-BisTris	natural abundance	20 mM
11	Protein	[U-99% 13C; U-99% 15N]	0.3 mM
12	H2O	natural abundance	95 %
13	D2O	natural abundance	5 %

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in E. coli

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	sodium acetate	natural abundance	20 mM
3	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	200 mM
4	sodium chloride	natural abundance	10 mM
5	Protein	[U-98% 13C; U-98% 15N]	0.5 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in CF system

#	Name	Isotope labeling	Concentration
8	DSS	natural abundance	0.5 mM
9	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	100 mM
10	Mes-BisTris	natural abundance	20 mM
11	Protein	[U-99% 13C; U-99% 15N]	0.3 mM
12	H2O	natural abundance	95 %
13	D2O	natural abundance	5 %

5 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in CF system

#	Name	Isotope labeling	Concentration
8	DSS	natural abundance	0.5 mM
9	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	100 mM
10	Mes-BisTris	natural abundance	20 mM
11	Protein	[U-99% 13C; U-99% 15N]	0.3 mM
12	H2O	natural abundance	95 %
13	D2O	natural abundance	5 %

6 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in CF system

#	Name	Isotope labeling	Concentration
8	DSS	natural abundance	0.5 mM
9	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	100 mM
10	Mes-BisTris	natural abundance	20 mM
11	Protein	[U-99% 13C; U-99% 15N]	0.3 mM
12	H2O	natural abundance	95 %
13	D2O	natural abundance	5 %

7 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in CF system

#	Name	Isotope labeling	Concentration
8	DSS	natural abundance	0.5 mM
9	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	100 mM
10	Mes-BisTris	natural abundance	20 mM
11	Protein	[U-99% 13C; U-99% 15N]	0.3 mM
12	H2O	natural abundance	95 %
13	D2O	natural abundance	5 %

8 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in CF system

#	Name	Isotope labeling	Concentration
8	DSS	natural abundance	0.5 mM
9	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	100 mM
10	Mes-BisTris	natural abundance	20 mM
11	Protein	[U-99% 13C; U-99% 15N]	0.3 mM
12	H2O	natural abundance	95 %
13	D2O	natural abundance	5 %

9 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 5.5, Details Protein expressed in CF system

#	Name	Isotope labeling	Concentration
8	DSS	natural abundance	0.5 mM
9	1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]	natural abundance	100 mM
10	Mes-BisTris	natural abundance	20 mM
11	Protein	[U-99% 13C; U-99% 15N]	0.3 mM
12	H2O	natural abundance	95 %
13	D2O	natural abundance	5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16947_2ksd.nef
Input source #2: Coordindates	2ksd.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-------100
MKQIRLLAQYYVDLMMKLGLVRFSMLLALALVVLAIVVQMAVTMVLHGQVESIDVIRSIFFGLLITPWAVYFLSVVVEQLEESRQRLSRLVQKLEEMRER
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKQIRLLAQYYVDLMMKLGLVRFSMLLALALVVLAIVVQMAVTMVLHGQVESIDVIRSIFFGLLITPWAVYFLSVVVEQLEESRQRLSRLVQKLEEMRER

-------110-----
DLSLNVQLKDNIAQL
|||||||||||||||
DLSLNVQLKDNIAQL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0

Content subtype: combined_16947_2ksd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	852		97.4 (chain: A, length: 115)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	73 (1)	noe	42.6 (chain: A, length: 115)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	123 (1)	pre	59.1 (chain: A, length: 115)
3	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	176 (1)	pre	60.0 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 97.4%
- Total number of assignments
  - ¹³C chemical shifts: 317
  - ¹H chemical shifts: 427
  - ¹⁵N chemical shifts: 108
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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 (%)
¹³C chemical shifts	562	317	56.4
¹H chemical shifts	735	425	57.8
¹⁵N chemical shifts	134	108	80.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	230	214	93.0
¹H chemical shifts	232	212	91.4
¹⁵N chemical shifts	114	108	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	332	103	31.0
¹H chemical shifts	503	213	42.3
¹⁵N chemical shifts	20	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	106	7	6.6
¹H chemical shifts	106	33	31.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	39	0	0.0
¹H chemical shifts	40	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 42.6%
- Total number of restraints: 73
- Weight of restraints: 1.0 (73)
- Potential type of restraints: upper-bound-parabolic (73)
- Range of distance target values: 3.0, 5.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: pre
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 59.1%
  - Total number of restraints: 123
  - Weight of restraints: 1.0 (123)
  - Potential type of restraints: upper-bound-parabolic (123)
  - Range of distance target values: 7.0, 25.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_4
    - Status: OK
    - Experiment type: pre
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 60.0%
    - Total number of restraints: 176
    - Weight of restraints: 1.0 (176)
    - Potential type of restraints: lower-bound-parabolic (176)
    - Range of distance target values: 4.0, 25.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Keywords cell-free synthesis, Histidine kinase receptor, membrane domain, two-helical hairpin

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Found 1 Document (0.709 seconds)

BMRB: 16947

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. histidine kinase receptor ArcB, : 1 : 3 : 2 entities Detail

Interaction partners 1. histidine kinase receptor ArcB, : 12 interactors Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail