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BMRB: 18399

2LRW

Solution structure of a ubiquitin-like protein from Trypanosoma brucei

Authors

Wang, R., Wang, T., Liao, S., Zhang, J., Tu, X.

Assembly

ubiqutin-like protein from Trypanosoma bucei

Entity

1. ubiqutin-like protein from Trypanosoma bucei (polymer, Thiol state: all free), 84 monomers, 9490.857 Da Detail

HHHHHHMLLK VKTVSNKVIQ ITSLTDDNTI AELKGKLEES EGIPGNMIRL VYQGKQLEDE KRLKDYQMSA GATFHMVVAL RAGC

Formula weight

9490.857 Da

Source organism

Trypanosoma brucei

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.9 %, Completeness: 71.6 %, Completeness (bb): 78.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.6 % (705 of 984)	76.6 % (392 of 512)	61.5 % (235 of 382)	86.7 % (78 of 90)
Backbone	78.1 % (392 of 502)	90.8 % (157 of 173)	64.2 % (158 of 246)	92.8 % (77 of 83)
Sidechain	68.8 % (385 of 560)	69.3 % (235 of 339)	69.6 % (149 of 214)	14.3 % (1 of 7)
Aromatic	0.0 % (0 of 54)	0.0 % (0 of 27)	0.0 % (0 of 27)
Methyl	66.0 % (66 of 100)	70.0 % (35 of 50)	62.0 % (31 of 50)

1. entity

HHHHHHMLLK VKTVSNKVIQ ITSLTDDNTI AELKGKLEES EGIPGNMIRL VYQGKQLEDE KRLKDYQMSA GATFHMVVAL RAGC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

LACS Plot; CA

Referencing offset: 0.08 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.08 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-04-21

Citation

Solution structure of a ubiqutin-like protein from Trypanosoma bucei
Wang, R., Liao, S., Wang, T., Zhang, J., Tu, X.
Not known

Related entities 1. ubiqutin-like protein from Trypanosoma bucei, : 1 : 1 : 639 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

2 2D 1H-13C HSQC

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

3 3D CBCA(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

4 3D C(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

5 3D HNCACB

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

6 3D H(CCO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

7 3D HBHA(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

8 3D 1H-15N NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

9 3D 1H-13C NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	tbubl	[U-100% 13C; U-100% 15N]		0.5 mM
2	H2O	natural abundance		0.5 mM
3	D2O	natural abundance		0.5 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18399_2lrw.nef
Input source #2: Coordindates	2lrw.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--------
HHHHHHMLLKVKTVSNKVIQITSLTDDNTIAELKGKLEESEGIPGNMIRLVYQGKQLEDEKRLKDYQMSAGATFHMVVALRAGC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HHHHHHMLLKVKTVSNKVIQITSLTDDNTIAELKGKLEESEGIPGNMIRLVYQGKQLEDEKRLKDYQMSAGATFHMVVALRAGC
--------10--------20--------30--------40--------50--------60--------70--------80----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	84	0	0	100.0

Content subtype: combined_18399_2lrw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	678		92.9 (chain: A, length: 84)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	814 (1)	noe	92.9 (chain: A, length: 84)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	101 (101)	.	82.1 (chain: A, length: 84)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 92.9%
- Total number of assignments
  - ¹H chemical shifts: 377
  - ¹³C chemical shifts: 224
  - ¹⁵N chemical shifts: 77
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 92.9%
- Total number of restraints: 814
- Weight of restraints: 1.0 (814)
- Potential type of restraints: square-well-parabolic (814)
- Range of distance target values: 2.4, 4.15 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 82.1%
- 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 protein