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Found 1 Document (0.78 seconds)

BMRB: 30127

5KP0

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,Flagellum-specific ATP synthase (E.C.3.6.3.14)

Entity

1. Flagellar protein FliT,Flagellum-specific ATP synthase (E.C.3.6.3.14) (polymer, Thiol state: not present), 140 monomers, 15643.89 Da Detail

MTSTVEFINR WQRIALLSQS LLELAQRGEW DLLLQQEVSY LQSIETVMEK QTPPGITRSI QDMVAGYIKQ TLDNEQLLKG LLQQRLDELS SLIGQVLFQG PSAGLVPRGS GGIEGMTTRL TRWLTALDNF EAKMALLPAV

Formula weight

15643.89 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: 99.3 %, Completeness: 59.9 %, Completeness (bb): 79.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	59.9 % (992 of 1655)	39.4 % (339 of 861)	80.3 % (513 of 639)	90.3 % (140 of 155)
Backbone	79.3 % (658 of 830)	50.3 % (144 of 286)	93.9 % (384 of 409)	96.3 % (130 of 135)
Sidechain	47.9 % (457 of 954)	33.9 % (195 of 575)	70.2 % (252 of 359)	50.0 % (10 of 20)
Aromatic	97.6 % (80 of 82)	97.6 % (40 of 41)	97.4 % (37 of 38)	100.0 % (3 of 3)
Methyl	92.7 % (178 of 192)	92.7 % (89 of 96)	92.7 % (89 of 96)

1. Flagellar protein FliT,Flagellum-specific ATP synthase

MTSTVEFINR WQRIALLSQS LLELAQRGEW DLLLQQEVSY LQSIETVMEK QTPPGITRSI QDMVAGYIKQ TLDNEQLLKG LLQQRLDELS SLIGQVLFQG PSAGLVPRGS GGIEGMTTRL TRWLTALDNF EAKMALLPAV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W protein, 20 mM potassium phosphate, 100 mM potassium chloride, 5 mM beta-mercaptoethanol, 0.5 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	protein	[U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W	0.5 mM
6	sodium azide	natural abundance	0.05 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-99% 13C; U-99% 15N; U-99% 2H] protein, 20 mM potassium phosphate, 100 mM potassium chloride, 5 mM beta-mercaptoethanol, 0.5 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	EDTA	natural abundance	0.5 mM
10	beta-mercaptoethanol	natural abundance	5 mM
11	potassium chloride	natural abundance	100 mM
12	potassium phosphate	natural abundance	20 mM
13	protein	[U-99% 13C; U-99% 15N; U-99% 2H]	0.5 mM
14	sodium azide	natural abundance	0.05 %
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

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: -0.05 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: -0.05 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: 0.06 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5KP0, Strand ID: A Detail

Release date

2016-08-10

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

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 30134 released on 2016-08-11
    Title Recognition and targeting mechanisms by chaperones in flagella assembly and operation
  BMRB: 30136 released on 2016-08-11
    Title Recognition and targeting mechanisms by chaperones in flagella assembly and operation

Related entities 1. Flagellar protein FliT,Flagellum-specific ATP synthase (E.C.3.6.3.14), : 1 : 2 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W protein, 20 mM potassium phosphate, 100 mM potassium chloride, 5 mM beta-mercaptoethanol, 0.5 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	protein	[U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W	0.5 mM
6	sodium azide	natural abundance	0.05 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	protein	[U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W	0.5 mM
6	sodium azide	natural abundance	0.05 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-99% 13C; U-99% 15N; U-99% 2H] protein, 20 mM potassium phosphate, 100 mM potassium chloride, 5 mM beta-mercaptoethanol, 0.5 mM EDTA, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	EDTA	natural abundance	0.5 mM
10	beta-mercaptoethanol	natural abundance	5 mM
11	potassium chloride	natural abundance	100 mM
12	potassium phosphate	natural abundance	20 mM
13	protein	[U-99% 13C; U-99% 15N; U-99% 2H]	0.5 mM
14	sodium azide	natural abundance	0.05 %
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

4 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	protein	[U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W	0.5 mM
6	sodium azide	natural abundance	0.05 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.5 mM
2	beta-mercaptoethanol	natural abundance	5 mM
3	potassium chloride	natural abundance	100 mM
4	potassium phosphate	natural abundance	20 mM
5	protein	[U-100% 15N,2H]_[1H,13C]ILVMATFY_[1H]W	0.5 mM
6	sodium azide	natural abundance	0.05 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D HNCO

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
9	EDTA	natural abundance	0.5 mM
10	beta-mercaptoethanol	natural abundance	5 mM
11	potassium chloride	natural abundance	100 mM
12	potassium phosphate	natural abundance	20 mM
13	protein	[U-99% 13C; U-99% 15N; U-99% 2H]	0.5 mM
14	sodium azide	natural abundance	0.05 %
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30127_5kp0.nef
Input source #2: Coordindates	5kp0.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-----------1010------1020-----
PSAGLVPRGSGGIEGMTTRLTRWLTALDNFEAKMALLPAV
||||||||||||||||||||||||||||||||||||||||
PSAGLVPRGSGGIEGMTTRLTRWLTALDNFEAKMALLPAV
-------110-------120-------130-------140

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	140	0	0	100.0

Content subtype: combined_30127_5kp0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	933		98.6 (chain: A, length: 140)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1286 (1)	noe	86.4 (chain: A, length: 140)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	1286 (1)	noe	86.4 (chain: A, length: 140)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	180 (1)	hbond	77.1 (chain: A, length: 140)
4	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	180 (1)	hbond	77.1 (chain: A, length: 140)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	216 (216)	.	82.9 (chain: A, length: 140)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	216 (216)	.	82.9 (chain: A, length: 140)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 294
  - ¹³C chemical shifts: 500
  - 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	861	294	34.1
¹³C chemical shifts	639	500	78.2
¹⁵N chemical shifts	163	139	85.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	286	129	45.1
¹³C chemical shifts	280	256	91.4
¹⁵N chemical shifts	135	129	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	575	165	28.7
¹³C chemical shifts	359	244	68.0
¹⁵N chemical shifts	28	10	35.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	93	92.1
¹³C chemical shifts	101	93	92.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	40	97.6
¹³C chemical shifts	38	37	97.4
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 86.4%
- Total number of restraints: 1282
- Weight of restraints: 1.0 (1282)
- Potential type of restraints: square-well-parabolic (1282)
- Range of distance target values: 2.29, 4.65 (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_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 86.4%
  - Total number of restraints: 1282
  - Weight of restraints: 1.0 (1282)
  - Potential type of restraints: square-well-parabolic (1282)
  - Range of distance target values: 2.29, 4.65 (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_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 77.1%
    - Total number of restraints: 180
    - Weight of restraints: 1.0 (180)
    - Potential type of restraints: square-well-parabolic (180)
    - Range of distance target values: 1.95, 2.85 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_7
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 77.1%
        --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTSTVEFINRWQRIALLSQSLLELAQRGEWDLLLQQEVSYLQSIETVMEKQTPPGITRSIQDMVAGYIKQTLDNEQLLKGLLQQRLDELSSLIGQVLFQG ||||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||||||||| MTSTVEFINRWQRIALLSQSLLELAQR..WD.LLQQEVSYLQSIETVME.......TRSIQDMVAGYIKQTLDNEQLLKGLLQQRLDELSSLIG...... --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-----------1010------1020----- PSAGLVPRGSGGIEGMTTRLTRWLTALDNFEAKMALLPAV |||||||||||||||||||||||| ............IEGMTTRLTRWLTALDNFEAKMAL -------110-----------1010------1020-
      - Total number of restraints: 180
        Total hydrogen bond restraints: 180
        O...H-x: 87
        O...h-N: 87
        Long range: 6
        O...H-x: 3
        O...h-N: 3
      - Weight of restraints: 1.0 (180)
        Total hydrogen bond restraints: 1.0 (180)
        O...H-x: 1.0 (87)
        O...h-N: 1.0 (87)
        Long range: 1.0 (6)
        O...H-x: 1.0 (3)
        O...h-N: 1.0 (3)
      - Potential type of restraints: square-well-parabolic (180)
        Total hydrogen bond restraints: square-well-parabolic (180)
        O...H-x: square-well-parabolic (87)
        O...h-N: square-well-parabolic (87)
        Long range: square-well-parabolic (6)
        O...H-x: square-well-parabolic (3)
        O...h-N: square-well-parabolic (3)
      - Range of distance target values: 1.95, 2.85 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 82.9%
- Total number of restraints: 216
- Total number of restraints per polymer type: 216
- Weight of restraints: 1.0 (216)
- Potential type of restraints: square-well-parabolic (216)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_6
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 82.9%
  - Total number of restraints: 216
  - Total number of restraints per polymer type: 216
  - Weight of restraints: 1.0 (216)
  - Potential type of restraints: square-well-parabolic (216)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords HYDROLASE, assembly factors, chaperones, flagella

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Found 1 Document (0.78 seconds)

BMRB: 30127

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. Flagellar protein FliT,Flagellum-specific ATP synthase (E.C.3.6.3.14), : 1 : 2 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

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NMR combined restraints 8 contents Detail