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BMRB: 17388

2L80

Solution Structure of the Zinc Finger Domain of USP13

Authors

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

Assembly

USP13

Entity

1. USP13 (polymer), 114 monomers, 12680.16 Da Detail

VSKYANNLTQ LDNGVRIPPS GWKCARCDLR ENLWLNLTDG SVLCGKWFFD SSGGNGHALE HYRDMGYPLA VKLGTITPDG ADVYSFQEEE PVLDPHLAKH LAHFGIDMLH MHGT

Formula weight

12680.16 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.9 %, Completeness: 80.8 %, Completeness (bb): 90.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.8 % (1049 of 1299)	80.9 % (541 of 669)	79.8 % (408 of 511)	84.0 % (100 of 119)
Backbone	90.6 % (609 of 672)	90.6 % (212 of 234)	90.3 % (298 of 330)	91.7 % (99 of 108)
Sidechain	73.4 % (535 of 729)	75.6 % (329 of 435)	72.4 % (205 of 283)	9.1 % (1 of 11)
Aromatic	4.4 % (6 of 136)	8.8 % (6 of 68)	0.0 % (0 of 65)	0.0 % (0 of 3)
Methyl	100.0 % (116 of 116)	100.0 % (58 of 58)	100.0 % (58 of 58)

1. entity

VSKYANNLTQ LDNGVRIPPS GWKCARCDLR ENLWLNLTDG SVLCGKWFFD SSGGNGHALE HYRDMGYPLA VKLGTITPDG ADVYSFQEEE PVLDPHLAKH LAHFGIDMLH MHGT

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	USP13	[U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 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	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.03 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.03 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 3.17 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2L80, Strand ID: A Detail

Release date

2011-12-13

Citation

Biochemical Characterization of the Ubiquitin Receptors in USP13 Reveals Different Catalytic Activation of Deubiquitination from Its Analogue USP5
Zhang, Y., Song, A., Zhou, C., Zhou, Z., Hu, H.
Not known

Related entities 1. USP13, : 1 : 2 : 4 : 45 entities Detail

Interaction partners 1. USP13, : 18 interactors Detail

More details for 18 interactors identified by 6 citations

Experiments performed 9 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	USP13	[U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 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	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

3 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	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		50 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

4 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	USP13	[U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D HNCO

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

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

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

8 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	USP13	[U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

9 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	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		50 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_17388_2l80.nef
Input source #2: Coordindates	2l80.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:59:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:46:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:26:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:29:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------1
GSVSKYANNLTQLDNGVRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHALEHYRDMGYPLAVKLGTITPDGADVYSFQEEEPVLDPHLA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSVSKYANNLTQLDNGVRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHALEHYRDMGYPLAVKLGTITPDGADVYSFQEEEPVLDPHLA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

00-------110----
KHLAHFGIDMLHMHGT
||||||||||||||||
KHLAHFGIDMLHMHGT
-------110------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	116	0	0	100.0

Content subtype: combined_17388_2l80.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1047		92.2 (chain: A, length: 116)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1413 (1)	noe	92.2 (chain: A, length: 116)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 92.2%
- Total number of assignments
  - ¹H chemical shifts: 542
  - ¹³C chemical shifts: 408
  - ¹⁵N chemical shifts: 97
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 92.2%
- Total number of restraints: 1413
- Weight of restraints: 1.0 (1413)
- Potential type of restraints: square-well-parabolic (1413)
- Range of distance target values: 1.59, 5.28 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords Ubiquitin binding, USP13, Zinc finger