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BMRB: 19670

2MI8

Solution structure of lysine-free (K0) ubiquitin

Authors

Huang, T., Li, J.R., Byrd, A.R.

Assembly

lysine-free (K0) ubiquitin

Entity

1. lysine-free (K0) ubiquitin (polymer, Thiol state: not present), 76 monomers, 8760.829 Da Detail

MQIFVRTLTG RTITLEVEPS DTIENVRARI QDREGIPPDQ QRLIFAGRQL EDGRTLSDYN IQRESTLHLV LRLRGG

Formula weight

8760.829 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 63.2 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	63.2 % (566 of 895)	57.1 % (269 of 471)	65.9 % (226 of 343)	87.7 % (71 of 81)
Backbone	97.1 % (437 of 450)	94.8 % (147 of 155)	98.6 % (219 of 222)	97.3 % (71 of 73)
Sidechain	38.4 % (198 of 515)	38.6 % (122 of 316)	39.8 % (76 of 191)	0.0 % (0 of 8)
Aromatic	0.0 % (0 of 32)	0.0 % (0 of 16)	0.0 % (0 of 16)
Methyl	10.2 % (10 of 98)	10.2 % (5 of 49)	10.2 % (5 of 49)

1. entity

MQIFVRTLTG RTITLEVEPS DTIENVRARI QDREGIPPDQ QRLIFAGRQL EDGRTLSDYN IQRESTLHLV LRLRGG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.22 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MI8, Strand ID: A Detail

Release date

2014-03-30

Citation

Solution structure of lysine-free (K0) ubiquitin
Huang, T., Li, J., Byrd, R.
Protein Sci. (2014), 23, 662-667, PubMed 24591328 , DOI 10.1002/pro.2450 , Abstract

Related entities 1. lysine-free (K0) ubiquitin, : 1 : 313 : 410 entities Detail

Interaction partners 1. lysine-free (K0) ubiquitin, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

2 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

5 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

7 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

8 3D HCACO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

9 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

10 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	K-free ubiquitin	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	D2O	[U-100% 2H]		5 %
4	H2O	natural abundance		95 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, RDC restraints	combined_19670_2mi8.nef
Input source #2: Coordindates	2mi8.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------
MQIFVRTLTGRTITLEVEPSDTIENVRARIQDREGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLRLRGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQIFVRTLTGRTITLEVEPSDTIENVRARIQDREGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLRLRGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_19670_2mi8.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	543		98.7 (chain: A, length: 76)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_2	OK	70 (70)	.	92.1 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 254
  - ¹³C chemical shifts: 219
  - ¹⁵N chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 92.1%
- Total number of restraints: 70
- Potential type of restraints: undefined (70)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords Lysine-free, ubiquitin