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Found 1 Document (0.662 seconds)

BMRB: 30134

5KRW

Recognition and targeting mechanisms by chaperones in flagella assembly and operation

Authors

Khanra, N.K., Rossi, P., Economou, A., Kalodimos, C.G.

Assembly

Flagellar protein FliT,Flagellar hook-associated protein 2

Entity

1. Flagellar protein FliT,Flagellar hook-associated protein 2 (polymer, Thiol state: not present), 155 monomers, 17374.61 Da Detail

MTSTVEFINR WQRIALLSQS LLELAQRGEW DLLLQQEVSY LQSIETVMEK QTPPGITRSI QDMVAGYIKQ TLDNEQLLKG LLQQRLDELS SLIGQVLFQG PSAGLVPRGS GGIEGSIDET VARYKAQFTQ LDTMMSKLNN TSSYLTQQFT AMNKS

Formula weight

17374.61 Da

Source organism

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.1 %, Completeness: 74.5 %, Completeness (bb): 87.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.5 % (1361 of 1828)	68.4 % (652 of 953)	80.5 % (563 of 699)	83.0 % (146 of 176)
Backbone	87.0 % (802 of 922)	83.3 % (264 of 317)	88.1 % (400 of 454)	91.4 % (138 of 151)
Sidechain	65.6 % (689 of 1050)	61.2 % (389 of 636)	75.1 % (292 of 389)	32.0 % (8 of 25)
Aromatic	70.8 % (68 of 96)	70.8 % (34 of 48)	69.6 % (32 of 46)	100.0 % (2 of 2)
Methyl	96.8 % (184 of 190)	96.8 % (92 of 95)	96.8 % (92 of 95)

1. entity 1

MTSTVEFINR WQRIALLSQS LLELAQRGEW DLLLQQEVSY LQSIETVMEK QTPPGITRSI QDMVAGYIKQ TLDNEQLLKG LLQQRLDELS SLIGQVLFQG PSAGLVPRGS GGIEGSIDET VARYKAQFTQ LDTMMSKLNN TSSYLTQQFT AMNKS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 7.0, Details 1 mM [U-99% 13C; U-99% 15N; U-99% 2H] FliT-FliD_fusion, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	FliT-FliD_fusion	[U-99% 13C; U-99% 15N; U-99% 2H]	1 mM
3	beta-mercaptoethanol	natural abundance	5 mM
4	potassium chloride	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	sodium azide	natural abundance	0.05 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 7.0, Details 1 mM U[15N,2H] 1H-13C-ILVMAT-methyl FliT-FliD_fusion, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.5 mM
8	FliT-FliD_fusion	U[15N,2H] 1H-13C-ILVMAT-methyl	1 mM
9	beta-mercaptoethanol	natural abundance	5 mM
10	potassium chloride	natural abundance	100 mM
11	potassium phosphate	natural abundance	20 mM
12	sodium azide	natural abundance	0.05 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 7.0, Details 1 mM [U-99% 13C; U-99% 15N] FliT-FliD_fusion, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	EDTA	natural abundance	0.5 mM
14	FliT-FliD_fusion	[U-99% 13C; U-99% 15N]	1 mM
15	beta-mercaptoethanol	natural abundance	5 mM
16	potassium chloride	natural abundance	100 mM
17	potassium phosphate	natural abundance	20 mM
18	sodium azide	natural abundance	0.05 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.3 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.3 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.35 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5KRW, Strand ID: A Detail

Release date

2016-08-11

Citation

Recognition and targeting mechanisms by chaperones in flagellum assembly and operation
Khanra, N.K., Rossi, P., Economou, A., Kalodimos, C.G.
Proc. Natl. Acad. Sci. U. S. A. (2016), 113, 9798-9803, PubMed 27528687 , DOI 10.1073/pnas.1607845113 , Abstract

Related entities 1. Flagellar protein FliT,Flagellar hook-associated protein 2, : 1 : 3 entities Detail

Experiments performed 10 experiments Detail

1 3D HNCO

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 7.0, Details 1 mM [U-99% 13C; U-99% 15N; U-99% 2H] FliT-FliD_fusion, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	FliT-FliD_fusion	[U-99% 13C; U-99% 15N; U-99% 2H]	1 mM
3	beta-mercaptoethanol	natural abundance	5 mM
4	potassium chloride	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	sodium azide	natural abundance	0.05 %

2 3D HNCACB

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	FliT-FliD_fusion	[U-99% 13C; U-99% 15N; U-99% 2H]	1 mM
3	beta-mercaptoethanol	natural abundance	5 mM
4	potassium chloride	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	sodium azide	natural abundance	0.05 %

3 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 7.0, Details 1 mM U[15N,2H] 1H-13C-ILVMAT-methyl FliT-FliD_fusion, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.5 mM
8	FliT-FliD_fusion	U[15N,2H] 1H-13C-ILVMAT-methyl	1 mM
9	beta-mercaptoethanol	natural abundance	5 mM
10	potassium chloride	natural abundance	100 mM
11	potassium phosphate	natural abundance	20 mM
12	sodium azide	natural abundance	0.05 %

4 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 7.0, Details 1 mM [U-99% 13C; U-99% 15N] FliT-FliD_fusion, 20 mM potassium phosphate, 100 mM potassium chloride, 0.5 mM EDTA, 5 mM beta-mercaptoethanol, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	EDTA	natural abundance	0.5 mM
14	FliT-FliD_fusion	[U-99% 13C; U-99% 15N]	1 mM
15	beta-mercaptoethanol	natural abundance	5 mM
16	potassium chloride	natural abundance	100 mM
17	potassium phosphate	natural abundance	20 mM
18	sodium azide	natural abundance	0.05 %

5 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
13	EDTA	natural abundance	0.5 mM
14	FliT-FliD_fusion	[U-99% 13C; U-99% 15N]	1 mM
15	beta-mercaptoethanol	natural abundance	5 mM
16	potassium chloride	natural abundance	100 mM
17	potassium phosphate	natural abundance	20 mM
18	sodium azide	natural abundance	0.05 %

6 3D HNCA

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	FliT-FliD_fusion	[U-99% 13C; U-99% 15N; U-99% 2H]	1 mM
3	beta-mercaptoethanol	natural abundance	5 mM
4	potassium chloride	natural abundance	100 mM
5	potassium phosphate	natural abundance	20 mM
6	sodium azide	natural abundance	0.05 %

7 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
13	EDTA	natural abundance	0.5 mM
14	FliT-FliD_fusion	[U-99% 13C; U-99% 15N]	1 mM
15	beta-mercaptoethanol	natural abundance	5 mM
16	potassium chloride	natural abundance	100 mM
17	potassium phosphate	natural abundance	20 mM
18	sodium azide	natural abundance	0.05 %

8 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.5 mM
8	FliT-FliD_fusion	U[15N,2H] 1H-13C-ILVMAT-methyl	1 mM
9	beta-mercaptoethanol	natural abundance	5 mM
10	potassium chloride	natural abundance	100 mM
11	potassium phosphate	natural abundance	20 mM
12	sodium azide	natural abundance	0.05 %

9 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.5 mM
8	FliT-FliD_fusion	U[15N,2H] 1H-13C-ILVMAT-methyl	1 mM
9	beta-mercaptoethanol	natural abundance	5 mM
10	potassium chloride	natural abundance	100 mM
11	potassium phosphate	natural abundance	20 mM
12	sodium azide	natural abundance	0.05 %

10 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
13	EDTA	natural abundance	0.5 mM
14	FliT-FliD_fusion	[U-99% 13C; U-99% 15N]	1 mM
15	beta-mercaptoethanol	natural abundance	5 mM
16	potassium chloride	natural abundance	100 mM
17	potassium phosphate	natural abundance	20 mM
18	sodium azide	natural abundance	0.05 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30134_5krw.nef
Input source #2: Coordindates	5krw.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
MTSTVEFINRWQRIALLSQSLLELAQRGEWDLLLQQEVSYLQSIETVMEKQTPPGITRSIQDMVAGYIKQTLDNEQLLKGLLQQRLDELSSLIGQVLFQG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MTSTVEFINRWQRIALLSQSLLELAQRGEWDLLLQQEVSYLQSIETVMEKQTPPGITRSIQDMVAGYIKQTLDNEQLLKGLLQQRLDELSSLIGQVLFQG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-----430-------440-------450-------460-------
PSAGLVPRGSGGIEGSIDETVARYKAQFTQLDTMMSKLNNTSSYLTQQFTAMNKS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
PSAGLVPRGSGGIEGSIDETVARYKAQFTQLDTMMSKLNNTSSYLTQQFTAMNKS
-------110-------120-------130-------140-------150-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	155	0	0	100.0

Content subtype: combined_30134_5krw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1237		94.8 (chain: A, length: 155)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	878 (1)	noe	63.2 (chain: A, length: 155)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	878 (1)	noe	63.2 (chain: A, length: 155)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	140 (1)	hbond	54.2 (chain: A, length: 155)
4	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	140 (1)	hbond	54.2 (chain: A, length: 155)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	221 (221)	.	58.7 (chain: A, length: 155)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_7	OK	221 (221)	.	58.7 (chain: A, length: 155)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 94.8%
- Total number of assignments
  - ¹H chemical shifts: 570
  - ¹³C chemical shifts: 528
  - ¹⁵N chemical shifts: 139
- 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	953	570	59.8
¹³C chemical shifts	699	528	75.5
¹⁵N chemical shifts	183	139	76.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	317	253	79.8
¹³C chemical shifts	310	262	84.5
¹⁵N chemical shifts	151	137	90.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	636	317	49.8
¹³C chemical shifts	389	266	68.4
¹⁵N chemical shifts	32	2	6.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	98	97.0
¹³C chemical shifts	101	98	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	32	66.7
¹³C chemical shifts	46	30	65.2
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 63.2%
- Total number of restraints: 878
- Weight of restraints: 1.0 (878)
- Potential type of restraints: square-well-parabolic (878)
- Range of distance target values: 2.3, 4.35 (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_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 63.2%
  - Total number of restraints: 878
  - Weight of restraints: 1.0 (878)
  - Potential type of restraints: square-well-parabolic (878)
  - Range of distance target values: 2.3, 4.35 (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_2
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 54.2%
    - Total number of restraints: 140
    - Weight of restraints: 1.0 (140)
    - Potential type of restraints: square-well-parabolic (140)
    - Range of distance target values: 2.05, 3.08 (Å)
    - Histogram of 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: 155, Sequence coverage: 54.2%
        --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTSTVEFINRWQRIALLSQSLLELAQRGEWDLLLQQEVSYLQSIETVMEKQTPPGITRSIQDMVAGYIKQTLDNEQLLKGLLQQRLDELSSLIGQVLFQG ||||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||||||||| MTSTVEFINRWQRIALLSQSLLELAQR..WD.LLQQEVSYLQSIETVME.......TRSIQDMVAGYIKQTLDNEQLLKGLLQQRLDELSSLIG --------10--------20--------30--------40--------50--------60--------70--------80--------90---- -------110-----430-------440-------450-------460------- PSAGLVPRGSGGIEGSIDETVARYKAQFTQLDTMMSKLNNTSSYLTQQFTAMNKS
      - Total number of restraints: 140
        Total hydrogen bond restraints: 140
        O...H-x: 70
        O...h-N: 70
      - Weight of restraints: 1.0 (140)
        Total hydrogen bond restraints: 1.0 (140)
        O...H-x: 1.0 (70)
        O...h-N: 1.0 (70)
      - Potential type of restraints: square-well-parabolic (140)
        Total hydrogen bond restraints: square-well-parabolic (140)
        O...H-x: square-well-parabolic (70)
        O...h-N: square-well-parabolic (70)
      - Range of distance target values: 2.05, 3.08 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 58.7%
- Total number of restraints: 221
- Total number of restraints per polymer type: 221
- Weight of restraints: 1.0 (221)
- Potential type of restraints: square-well-parabolic (221)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_7
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 58.7%
  - Total number of restraints: 221
  - Total number of restraints per polymer type: 221
  - Weight of restraints: 1.0 (221)
  - Potential type of restraints: square-well-parabolic (221)
  - Plot of Phi-Psi angle restraints
  - Plot of Chi1-Chi2 angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords CHAPERONE, Flagella, assembly factors, chaperones

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Found 1 Document (0.662 seconds)

BMRB: 30134

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Flagellar protein FliT,Flagellar hook-associated protein 2, : 1 : 3 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 8 contents Detail