Evidence: gel filtration, in addition 15N relaxation rates T1 & T2 by NMR
Type
Name
Symmetry operation
Number
identity operation
1_555
1
Buried area
0 Å2
ΔGint
0 kcal/mol
Surface area
7890 Å2
Method
PISA
NMR ensembles
Data
Criteria
Number of conformers (submitted / calculated)
20 / 100
structures with the lowest energy
Representative
Model #1
lowest energy
-
Components
#1: Protein
UBXdomain-containingprotein6 / UBX domain-containing protein 1
Mass: 13822.567 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first 4 residues represent a cloning artifact. / Source: (gene. exp.) Homo sapiens (human) / Gene: UBXN6, UBXD1, UBXDC2 / Plasmid: pET28a Details (production host): encodes for His6-Tag with Thrombin cleavage site Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9BZV1
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
isotropic
1
2D 1H-15N HSQC
1
2
2
isotropic
1
2D 1H-13C HSQC aliphatic
1
3
1
isotropic
1
3DCBCA(CO)NH
1
4
1
isotropic
1
3D HN(CA)CB
1
5
1
isotropic
1
3D HNCO
1
6
1
isotropic
1
3DHN(CA)CO
1
7
1
isotropic
1
3DH(CCO)NH
1
8
1
isotropic
1
3DC(CO)NH
1
9
1
isotropic
1
3D 1H-15N TOCSY
1
10
3
isotropic
1
3D 1H-15N NOESY
1
11
2
isotropic
1
3D (H)CCH-COSY aliphatic
1
12
2
isotropic
1
3D (H)CCH-TOCSY aliphatic
1
13
1
isotropic
1
3D (H)CCH-TOCSY
1
14
1
isotropic
1
3D 1H-13C NOESY aliphatic
1
15
1
isotropic
1
3D 1H-13C NOESY aromatic
1
16
1
isotropic
1
2D Histidin H(C)N-SOFAST-HMQC
-
Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
solution
1
900 uM [U-98% 13C; U-98% 15N] UBXD1 PUB domain, 16 mM potassium phosphate, 34 mM sodium phosphate, 90 % H2O, 10 % [U-99% 2H] D2O, 0.1 mM DSS, 90% H2O/10% D2O
13C_15N_H2O
90% H2O/10% D2O
solution
2
500 uM [U-98% 13C; U-98% 15N] UBXD1 PUB domain, 16 mM potassium phosphate, 34 mM sodium phosphate, 100 % [U-99% 2H] D2O, 0.1 mM DSS, 100% D2O
13C_15N_D2O
100% D2O
solution
3
700 uM [U-98% 15N] UBXD1 PUB domain, 16 mM potassium phosphate, 34 mM sodium phosphate, 90 % H2O, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O
15N_H2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
900uM
UBXD1PUBdomain
[U-98% 13C; U-98% 15N]
1
16mM
potassiumphosphate
naturalabundance
1
34mM
sodiumphosphate
naturalabundance
1
90 %
H2O
naturalabundance
1
10 %
D2O
[U-99% 2H]
1
0.1mM
DSS
naturalabundance
1
500uM
UBXD1PUBdomain
[U-98% 13C; U-98% 15N]
2
16mM
potassiumphosphate
naturalabundance
2
34mM
sodiumphosphate
naturalabundance
2
100 %
D2O
[U-99% 2H]
2
0.1mM
DSS
naturalabundance
2
700uM
UBXD1PUBdomain
[U-98% 15N]
3
16mM
potassiumphosphate
naturalabundance
3
34mM
sodiumphosphate
naturalabundance
3
90 %
H2O
naturalabundance
3
10 %
D2O
[U-99% 2H]
3
Sample conditions
Ionic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
-
NMR measurement
NMR spectrometer
Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz / Details: TCI cryoprobe
-
Processing
NMR software
Name
Version
Developer
Classification
TopSpin
3.5
BrukerBiospin
collection
TopSpin
BrukerBiospin
processing
CARA
1.6
KellerandWuthrich
chemicalshiftassignment
UNIO
10
Herrmann
peakpicking
CYANA
3.98.9
Guntert, MumenthalerandWuthrich
structurecalculation
YASARA
11.12.31
Krieger
refinement
Refinement
Method: molecular dynamics / Software ordinal: 6
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20
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