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BMRB: 19523

2MEK

N-terminal domain of Bilbo1 from Trypanosoma brucei

Authors

Vidilaseris, K., Morriswood, B., Kontaxis, G., Dong, G.

Assembly

N-terminal domain of Bilbo1 from Trypanosoma brucei

Entity

1. N-terminal domain of Bilbo1 from Trypanosoma brucei (polymer), 110 monomers, 12883.42 Da Detail

MAFLVQVAAD IFNNKVNFEL SFPSRPSISE LTRSAETAFS NEISLRRPDN VPSHKFHSSK IKMYDEELNK WVDLIREDQL TDYCQLYVFQ PPNEWHKESQ KEIPPAMKPP

Formula weight

12883.42 Da

Source organism

Trypanosoma brucei

Exptl. method

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.5 %, Completeness: 76.3 %, Completeness (bb): 92.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.3 % (1032 of 1352)	71.4 % (509 of 713)	79.4 % (417 of 525)	93.0 % (106 of 114)
Backbone	92.3 % (591 of 640)	94.3 % (198 of 210)	89.4 % (295 of 330)	98.0 % (98 of 100)
Sidechain	65.7 % (540 of 822)	61.8 % (311 of 503)	72.5 % (221 of 305)	57.1 % (8 of 14)
Aromatic	73.8 % (96 of 130)	76.9 % (50 of 65)	69.8 % (44 of 63)	100.0 % (2 of 2)
Methyl	98.0 % (96 of 98)	98.0 % (48 of 49)	98.0 % (48 of 49)

1. Bil NTD

MAFLVQVAAD IFNNKVNFEL SFPSRPSISE LTRSAETAFS NEISLRRPDN VPSHKFHSSK IKMYDEELNK WVDLIREDQL TDYCQLYVFQ PPNEWHKESQ KEIPPAMKPP

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

LACS Plot; CA

Referencing offset: 0.89 ppm, Outliers: 4 Detail

LACS Plot; CB

Referencing offset: 0.89 ppm, Outliers: 4 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.21 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2014-01-01

Citation

Structure of the TbBILBO1 protein N-terminal domain from Trypanosoma brucei reveals an essential requirement for a conserved surface patch
Vidilaseris, K., Morriswood, B., Kontaxis, G., Dong, G.
J. Biol. Chem. (2014), 289, 3724-3735, PubMed 24362019 , DOI 10.1074/jbc.M113.529032 , Abstract

Related entities 1. N-terminal domain of Bilbo1 from Trypanosoma brucei, : 1 : 1 : 19 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

2 2D 1H-13C HSQC aliphatic

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

3 2D 1H-13C HSQC aromatic

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

4 3D HNCO

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

5 3D HNCA

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

6 3D HN(CO)CA

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

7 3D HCACO

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

8 3D HNCACB

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

9 3D CBCA(CO)NH

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

10 3D HCCH-TOCSY

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

11 3D 1H-15N NOESY

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

12 3D 1H-15N TOCSY

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

13 3D 1H-13C NOESY

Instrument

Varian Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	BILBO1-NTD	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	[U-2H]		10 %
5	H2O	natural abundance		90 %
6	sodium azide	natural abundance		0.2 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19523_2mek.nef
Input source #2: Coordindates	2mek.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
MAFLVQVAADIFNNKVNFELSFPSRPSISELTRSAETAFSNEISLRRPDNVPSHKFHSSKIKMYDEELNKWVDLIREDQLTDYCQLYVFQPPNEWHKESQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAFLVQVAADIFNNKVNFELSFPSRPSISELTRSAETAFSNEISLRRPDNVPSHKFHSSKIKMYDEELNKWVDLIREDQLTDYCQLYVFQPPNEWHKESQ

-------110
KEIPPAMKPP
||||||||||
KEIPPAMKPP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	110	0	0	100.0

Content subtype: combined_19523_2mek.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1009		94.5 (chain: A, length: 110)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1904 (1)	noe	89.1 (chain: A, length: 110)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	35 (1)	undefined	19.1 (chain: A, length: 110)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	140 (140)	.	87.3 (chain: A, length: 110)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 94.5%
- Total number of assignments
  - ¹H chemical shifts: 493
  - ¹³C chemical shifts: 409
  - ¹⁵N chemical shifts: 107
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 89.1%
- Total number of restraints: 1899
- Weight of restraints: 1.0 (1899)
- Potential type of restraints: square-well-parabolic (1899)
- Range of distance target values: 1.88, 7.57 (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: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 19.1%
  - Total number of restraints: 35
  - Weight of restraints: 1.0 (35)
  - Potential type of restraints: square-well-parabolic (35)
  - Range of distance target values: 5.0, 5.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 87.3%
- Total number of restraints: 140
- Total number of restraints per polymer type: 140
- Weight of restraints: 1.0 (140)
- Potential type of restraints: square-well-parabolic (140)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Bilbo1, N-terminal domain, Trypanosoma brucei