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BMRB: 25088

2MWS

NMR solution structure of the Ubiquitin like domain (UBL) of DNA-damage-inducible 1 protein (Ddi1)

Authors

Nowicka, U., Fushman, D., Chen, T.

Assembly

Ddi1UBL

Entity

1. Ddi1UBL (polymer, Thiol state: all free), 79 monomers, 8819.866 Da Detail

DLTISNELTG EIYGPIEVSE DMALTDLIAL LQADCGFDKT KHDLYYNMDI LDSNRTQSLK ELGLKTDDLL LIRGKISNS

Formula weight

8819.866 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.8 %, Completeness (bb): 99.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.8 % (884 of 904)	99.6 % (464 of 466)	94.9 % (336 of 354)	100.0 % (84 of 84)
Backbone	99.8 % (471 of 472)	100.0 % (162 of 162)	99.6 % (231 of 232)	100.0 % (78 of 78)
Sidechain	96.0 % (486 of 506)	99.3 % (302 of 304)	90.8 % (178 of 196)	100.0 % (6 of 6)
Aromatic	63.2 % (24 of 38)	100.0 % (19 of 19)	26.3 % (5 of 19)
Methyl	99.1 % (105 of 106)	100.0 % (53 of 53)	98.1 % (52 of 53)

1. Ddi1UBL

DLTISNELTG EIYGPIEVSE DMALTDLIAL LQADCGFDKT KHDLYYNMDI LDSNRTQSLK ELGLKTDDLL LIRGKISNS

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295.5 K, pH 6.8, Details 1mM Ddi1UBL sample in pH6.8 20mM Sodium Phosphate Buffer, with 3mM TCEP, containing 5% D2O.

#	Name	Isotope labeling	Concentration
1	Ddi1UBL	[U-100% 15N]	1 mM
2	D2O	[U-99% 2H]	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM
5	TCEP	natural abundance	3 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295.5 K, pH 6.8, Details 1mM Ddi1UBL sample in pH6.8 20mM Sodium Phosphate Buffer, with 3mM TCEP, containing 5% D2O.

#	Name	Isotope labeling	Concentration
6	Ddi1UBL	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-99% 2H]	5 %
8	H2O	natural abundance	95 %
9	sodium phosphate	natural abundance	20 mM
10	TCEP	natural abundance	3 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295.5 K, pH 6.8, Details 1mM Ddi1UBL sample in liquid crystalline medium

#	Name	Isotope labeling	Concentration
11	Ddi1UBL	[U-100% 15N]	1 mM
12	D2O	[U-99% 2H]	5 %
13	H2O	natural abundance	45 %
14	sodium phosphate	natural abundance	10 mM
15	TCEP	natural abundance	3 mM
16	C12E5	natural abundance	5 %
17	n-hexanol	natural abundance	45 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	TMS	methyl protons	internal	indirect	0.1013291
¹³C	TMS	methyl protons	internal	indirect	0.25145

Referencing offset: 2.15 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	TMS	methyl protons	internal	indirect	0.1013291
¹³C	TMS	methyl protons	internal	indirect	0.25145

Referencing offset: 2.15 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	TMS	methyl protons	internal	indirect	0.1013291
¹³C	TMS	methyl protons	internal	indirect	0.25145

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	TMS	methyl protons	internal	indirect	0.1013291
¹³C	TMS	methyl protons	internal	indirect	0.25145

Referencing offset: 2.43 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 8 models in PDB: 2MWS, Strand ID: B Detail

Release date

2015-03-22

Citation

DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin
Nowicka, U., Zhang, D., Walker, O., Castaneda, C.A., Krutauz, D., Chen, T., Reis, N., Glickman, M.H., Fushman, D.
Structure (2015), 23, 542-557, PubMed 25703377 , DOI 10.1016/j.str.2015.01.010 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25066 released on 2015-02-01
Title NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1)

Related entities 1. Ddi1UBL, : 1 : 4 : 6 entities Detail

Interaction partners 1. Ddi1UBL, : 10 interactors Detail

More details for 10 interactors identified by 7 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295.5 K, pH 6.8, Details 1mM Ddi1UBL sample in pH6.8 20mM Sodium Phosphate Buffer, with 3mM TCEP, containing 5% D2O.

#	Name	Isotope labeling	Concentration
1	Ddi1UBL	[U-100% 15N]	1 mM
2	D2O	[U-99% 2H]	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM
5	TCEP	natural abundance	3 mM

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Ddi1UBL	[U-100% 15N]	1 mM
2	D2O	[U-99% 2H]	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM
5	TCEP	natural abundance	3 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Ddi1UBL	[U-100% 15N]	1 mM
2	D2O	[U-99% 2H]	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM
5	TCEP	natural abundance	3 mM

4 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Ddi1UBL	[U-100% 15N]	1 mM
2	D2O	[U-99% 2H]	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM
5	TCEP	natural abundance	3 mM

5 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Ddi1UBL	[U-100% 15N]	1 mM
2	D2O	[U-99% 2H]	5 %
3	H2O	natural abundance	95 %
4	sodium phosphate	natural abundance	20 mM
5	TCEP	natural abundance	3 mM

6 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Ddi1UBL	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-99% 2H]	5 %
8	H2O	natural abundance	95 %
9	sodium phosphate	natural abundance	20 mM
10	TCEP	natural abundance	3 mM

7 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Ddi1UBL	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-99% 2H]	5 %
8	H2O	natural abundance	95 %
9	sodium phosphate	natural abundance	20 mM
10	TCEP	natural abundance	3 mM

8 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Ddi1UBL	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-99% 2H]	5 %
8	H2O	natural abundance	95 %
9	sodium phosphate	natural abundance	20 mM
10	TCEP	natural abundance	3 mM

9 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Ddi1UBL	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-99% 2H]	5 %
8	H2O	natural abundance	95 %
9	sodium phosphate	natural abundance	20 mM
10	TCEP	natural abundance	3 mM

10 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Ddi1UBL	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-99% 2H]	5 %
8	H2O	natural abundance	95 %
9	sodium phosphate	natural abundance	20 mM
10	TCEP	natural abundance	3 mM

11 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Ddi1UBL	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-99% 2H]	5 %
8	H2O	natural abundance	95 %
9	sodium phosphate	natural abundance	20 mM
10	TCEP	natural abundance	3 mM

12 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	Ddi1UBL	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-99% 2H]	5 %
8	H2O	natural abundance	95 %
9	sodium phosphate	natural abundance	20 mM
10	TCEP	natural abundance	3 mM

13 RDC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295.5 K, pH 6.8, Details 1mM Ddi1UBL sample in liquid crystalline medium

#	Name	Isotope labeling	Concentration
11	Ddi1UBL	[U-100% 15N]	1 mM
12	D2O	[U-99% 2H]	5 %
13	H2O	natural abundance	45 %
14	sodium phosphate	natural abundance	10 mM
15	TCEP	natural abundance	3 mM
16	C12E5	natural abundance	5 %
17	n-hexanol	natural abundance	45 %

14 RDC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 315 K, pH 6.8, Details 1mM Ddi1UBL sample in liquid crystalline medium

#	Name	Isotope labeling	Concentration
11	Ddi1UBL	[U-100% 15N]	1 mM
12	D2O	[U-99% 2H]	5 %
13	H2O	natural abundance	45 %
14	sodium phosphate	natural abundance	10 mM
15	TCEP	natural abundance	3 mM
16	C12E5	natural abundance	5 %
17	n-hexanol	natural abundance	45 %

nullKeywords DNA-damage-inducible 1 protein, Ddi1, Ubiquitin like domain, UBL, NMR

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Found 1 Document (0.828 seconds)

BMRB: 25088

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Ddi1UBL, : 1 : 4 : 6 entities Detail

Interaction partners 1. Ddi1UBL, : 10 interactors Detail

Experiments performed 14 experiments Detail

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