BMRBj - BMREntryMaster

Found 1 Document (0.876 seconds)

BMRB: 17554

2LBC

solution structure of tandem UBA of USP13

Authors

Zhang, Y., Zhou, C., Zhou, Z., Song, A., Hun, H.

Assembly

tandem UBA of USP13

Entity

1. tandem UBA of USP13 (polymer), 126 monomers, 13762.19 Da Detail

DIDESSVMQL AEMGFPLEAC RKAVYFTGNM GAEVAFNWII VHMEEPDFAE PLTMPGYGGA ASAGASVFGA SGLDNQPPEE IVAIITSMGF QRNQAIQALR ATNNNLERAL DWIFSHPEFE EDSDFV

Formula weight

13762.19 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 77.6 %, Completeness (bb): 84.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.6 % (1094 of 1410)	81.6 % (591 of 724)	69.4 % (384 of 553)	89.5 % (119 of 133)
Backbone	84.8 % (629 of 742)	96.1 % (245 of 255)	72.0 % (265 of 368)	100.0 % (119 of 119)
Sidechain	74.1 % (581 of 784)	73.8 % (346 of 469)	78.1 % (235 of 301)	0.0 % (0 of 14)
Aromatic	14.5 % (20 of 138)	17.4 % (12 of 69)	11.9 % (8 of 67)	0.0 % (0 of 2)
Methyl	98.4 % (126 of 128)	98.4 % (63 of 64)	98.4 % (63 of 64)

1. tandem UBA of USP13

DIDESSVMQL AEMGFPLEAC RKAVYFTGNM GAEVAFNWII VHMEEPDFAE PLTMPGYGGA ASAGASVFGA SGLDNQPPEE IVAIITSMGF QRNQAIQALR ATNNNLERAL DWIFSHPEFE EDSDFV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		20 mM
2	sodium chloride	natural abundance		50 mM
3	entity	[U-100% 15N]		1 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	sodium phosphate	natural abundance		20 mM
7	sodium chloride	natural abundance		50 mM
8	entity	[U-100% 13C; U-100% 15N]		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2LBC, Strand ID: A Detail

Release date

2012-03-04

Citation

Domain analysis reveals that a deubiquitinating enzyme USP13 performs non-activating catalysis for Lys63-linked polyubiquitin
Zhang, Y., Zhou, C., Zhou, Z., Song, A., Hu, H.
PLoS One (2011), 6, e29362-e29362, PubMed 22216260 , DOI 10.1371/journal.pone.0029362 , Abstract

Related entities 1. tandem UBA of USP13, : 1 : 2 : 40 entities Detail

Interaction partners 1. tandem UBA of USP13, : 18 interactors Detail

More details for 18 interactors identified by 6 citations

Experiments performed 8 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 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		20 mM
2	sodium chloride	natural abundance		50 mM
3	entity	[U-100% 15N]		1 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	sodium phosphate	natural abundance		20 mM
7	sodium chloride	natural abundance		50 mM
8	entity	[U-100% 13C; U-100% 15N]		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	sodium phosphate	natural abundance		20 mM
7	sodium chloride	natural abundance		50 mM
8	entity	[U-100% 13C; U-100% 15N]		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

4 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	sodium phosphate	natural abundance		20 mM
7	sodium chloride	natural abundance		50 mM
8	entity	[U-100% 13C; U-100% 15N]		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

5 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		20 mM
2	sodium chloride	natural abundance		50 mM
3	entity	[U-100% 15N]		1 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	sodium phosphate	natural abundance		20 mM
7	sodium chloride	natural abundance		50 mM
8	entity	[U-100% 13C; U-100% 15N]		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		20 mM
2	sodium chloride	natural abundance		50 mM
3	entity	[U-100% 15N]		1 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	sodium phosphate	natural abundance		20 mM
7	sodium chloride	natural abundance		50 mM
8	entity	[U-100% 13C; U-100% 15N]		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17554_2lbc.nef
Input source #2: Coordindates	2lbc.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--------80--------90-------100
DIDESSVMQLAEMGFPLEACRKAVYFTGNMGAEVAFNWIIVHMEEPDFAEPLTMPGYGGAASAGASVFGASGLDNQPPEEIVAIITSMGFQRNQAIQALR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DIDESSVMQLAEMGFPLEACRKAVYFTGNMGAEVAFNWIIVHMEEPDFAEPLTMPGYGGAASAGASVFGASGLDNQPPEEIVAIITSMGFQRNQAIQALR

-------110-------120------
ATNNNLERALDWIFSHPEFEEDSDFV
||||||||||||||||||||||||||
ATNNNLERALDWIFSHPEFEEDSDFV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	126	0	0	100.0

Content subtype: combined_17554_2lbc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1053		100.0 (chain: A, length: 126)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1635 (1)	noe	95.2 (chain: A, length: 126)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 583
  - ¹³C chemical shifts: 351
  - ¹⁵N chemical shifts: 119
- 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: 126, Sequence coverage: 95.2%
- Total number of restraints: 1635
- Weight of restraints: 1.0 (1635)
- Potential type of restraints: square-well-parabolic (1635)
- Range of distance target values: 1.56, 6.96 (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

Keywords tandem UBA of USP13