BMRBj - BMREntryMaster

Found 1 Document (0.792 seconds)

BMRB: 26901

6KCZ

1H, 13C and 15N backbone and side-chain resonance assignments of the ZnF UBP domain of USP20/VDU2

Authors

Yang, Y., Wen, Y., Zhang, N.

Assembly

USP20

Entity

1. USP20 (polymer, Thiol state: unknown), 102 monomers, 11152.62 Da Detail

GSHMGDSRDL CPHLDSIGEV TKEDLLLKSK GTCQSCGVTG PNLWACLQVA CPYVGCGESF ADHSTIHAQA KKHNLTVNLT TFRLWCYACE KEVFLEQRLA AP

Formula weight

11152.62 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 85.1 %, Completeness (bb): 96.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.1 % (969 of 1138)	82.6 % (483 of 585)	87.7 % (391 of 446)	88.8 % (95 of 107)
Backbone	96.5 % (583 of 604)	96.6 % (201 of 208)	96.3 % (287 of 298)	96.9 % (95 of 98)
Sidechain	76.0 % (477 of 628)	74.8 % (282 of 377)	80.6 % (195 of 242)	0.0 % (0 of 9)
Aromatic	4.4 % (4 of 90)	4.4 % (2 of 45)	4.7 % (2 of 43)	0.0 % (0 of 2)
Methyl	100.0 % (110 of 110)	100.0 % (55 of 55)	100.0 % (55 of 55)

1. USP20

GSHMGDSRDL CPHLDSIGEV TKEDLLLKSK GTCQSCGVTG PNLWACLQVA CPYVGCGESF ADHSTIHAQA KKHNLTVNLT TFRLWCYACE KEVFLEQRLA AP

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	D2O	natural abundance	100 %
9	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
10	Na2HPO4/NaH2PO4	natural abundance	20 mM
11	NaCl	natural abundance	100 mM
12	DTT	natural abundance	2 mM
13	ZnSO4	natural abundance	50 uM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.12 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.12 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.63 ppm, Outliers: 1 Detail

Release date

2016-09-18

Citation

¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of the ZnF-UBP domain of USP20/VDU2
Yang, Y., Wen, Y., Zhang, N.
Biomol. NMR Assign. (2017), 11, 91-93, PubMed 28091961 , DOI 10.1007/s12104-017-9726-y , Abstract

Related entities 1. USP20, : 1 : 3 : 91 entities Detail

Interaction partners 1. USP20, : 14 interactors Detail

More details for 14 interactors identified by 4 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	D2O	natural abundance	100 %
9	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
10	Na2HPO4/NaH2PO4	natural abundance	20 mM
11	NaCl	natural abundance	100 mM
12	DTT	natural abundance	2 mM
13	ZnSO4	natural abundance	50 uM

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

4 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

7 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

9 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	D2O	natural abundance	100 %
9	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
10	Na2HPO4/NaH2PO4	natural abundance	20 mM
11	NaCl	natural abundance	100 mM
12	DTT	natural abundance	2 mM
13	ZnSO4	natural abundance	50 uM

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	D2O	natural abundance	100 %
9	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
10	Na2HPO4/NaH2PO4	natural abundance	20 mM
11	NaCl	natural abundance	100 mM
12	DTT	natural abundance	2 mM
13	ZnSO4	natural abundance	50 uM

13 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 %
2	H2O	natural abundance	90 %
3	USP20	[U-100% 13C; U-100% 15N]	0.6 ~ 0.8 mM
4	Na2HPO4/NaH2PO4	natural abundance	20 mM
5	NaCl	natural abundance	100 mM
6	DTT	natural abundance	2 mM
7	ZnSO4	natural abundance	50 uM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr26901_3.str
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

Content subtype: bmr26901_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1073		96.1 (chain: 1, length: 102)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 102, Sequence coverage: 96.1%
- Total number of assignments
  - ¹H chemical shifts: 589
  - ¹³C chemical shifts: 389
  - ¹⁵N chemical shifts: 95
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	585	479	81.9
¹³C chemical shifts	446	389	87.2
¹⁵N chemical shifts	110	95	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	200	96.2
¹³C chemical shifts	204	196	96.1
¹⁵N chemical shifts	98	95	96.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	377	279	74.0
¹³C chemical shifts	242	193	79.8
¹⁵N chemical shifts	12	0	0.0

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Found 1 Document (0.792 seconds)

BMRB: 26901

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. USP20, : 1 : 3 : 91 entities Detail

Interaction partners 1. USP20, : 14 interactors Detail

Experiments performed 13 experiments Detail

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Chemical shift validation 3 contents Detail