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BMRB: 15988

2K9K

TonB2 PROTEIN FROM Vibrio anguillarum

Authors

Lopez, C.S., Peacock, S.R., Crosa, J.H., Vogel, H.J.

Assembly

TonB2-CTD

Entity

1. TonB2-CTD (polymer, Thiol state: not present), 106 monomers, 11832.42 Da Detail

AHPFTSAPTF GDFGSNQQAM PLYRVEPVYP SRALKRGVEG FVTLSFTIDT TGKAVDINVV DANPKRMFER EAMQALKKWK YQPQIVDGKA IEQPGQTVTV EFKIAK

Formula weight

11832.42 Da

Source organism

Vibrio anguillarum

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.2 %, Completeness: 74.5 %, Completeness (bb): 80.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.5 % (937 of 1258)	82.0 % (539 of 657)	60.4 % (297 of 492)	92.7 % (101 of 109)
Backbone	80.8 % (501 of 620)	94.3 % (199 of 211)	66.9 % (208 of 311)	95.9 % (94 of 98)
Sidechain	72.0 % (531 of 737)	76.2 % (340 of 446)	65.7 % (184 of 280)	63.6 % (7 of 11)
Aromatic	26.4 % (29 of 110)	50.9 % (28 of 55)	0.0 % (0 of 54)	100.0 % (1 of 1)
Methyl	90.2 % (101 of 112)	91.1 % (51 of 56)	89.3 % (50 of 56)

1. TonB2-CTD

AHPFTSAPTF GDFGSNQQAM PLYRVEPVYP SRALKRGVEG FVTLSFTIDT TGKAVDINVV DANPKRMFER EAMQALKKWK YQPQIVDGKA IEQPGQTVTV EFKIAK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

LACS Plot; CA

Referencing offset: -0.6 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.6 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K9K, Strand ID: A Detail

Release date

2008-10-15

Citation

Molecular characterization of the TonB2 protein from the fish pathogen Vibrio anguillarum
Lopez, C.S., Peacock, S.R., Crosa, J.H., Vogel, H.J.
Biochem. J. (2009), 418, 49-59, PubMed 18973471 , DOI 10.1042/BJ20081462 , Abstract

Related entities 1. TonB2-CTD, : 1 : 8 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

4 3D C(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

5 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

6 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

7 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

9 3D H(CCO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

10 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TonB2-CTD	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		90 %
3	DSS	natural abundance		1 mM
4	H2O	natural abundance		10 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15988_2k9k.nef
Input source #2: Coordindates	2k9k.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

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
DHPFTSAPTFGDFGSNQQAMPLYRVEPVYPSRALKRGVEGFVTLSFTIDTTGKAVDINVVDANPKRMFEREAMQALKKWKYQPQIVDGKAIEQPGQTVTV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DHPFTSAPTFGDFGSNQQAMPLYRVEPVYPSRALKRGVEGFVTLSFTIDTTGKAVDINVVDANPKRMFEREAMQALKKWKYQPQIVDGKAIEQPGQTVTV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------
EFKIAK
||||||
EFKIAK
------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	106	0	0	100.0

Content subtype: combined_15988_2k9k.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assignments_tonb2	Warning	968		96.2 (chain: A, length: 106)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2099 (1)	noe	85.8 (chain: A, length: 106)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	46 (1)	hbond	28.3 (chain: A, length: 106)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	101 (101)	.	78.3 (chain: A, length: 106)

Assigned chemical shifts

Saveframe: assignments_tonb2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 96.2%
- Total number of assignments
  - ¹H chemical shifts: 589
  - ¹³C chemical shifts: 279
  - ¹⁵N chemical shifts: 100
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 85.8%
- Total number of restraints: 2094
- Weight of restraints: 1.0 (2094)
- Potential type of restraints: upper-bound-parabolic (2094)
- Range of distance target values: 2.3, 5.5 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 28.3%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: upper-bound-parabolic (46)
  - Range of distance target values: 2.3, 3.3 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 78.3%
- Total number of restraints: 101
- Total number of restraints per polymer type: 101
- Weight of restraints: 1.0 (101)
- Potential type of restraints: square-well-parabolic (101)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords TonB2-CTD