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BMRB: 25219

2MUL

Solution Structure of the UBM1 domain of human HUWE1/ARF-BP1

Authors

Farhadi, S., Khatun, R., Lemak, A., Kaustov, L., Ramabadran, R., Hunter, H., Sheng, Y.

Assembly

UBM1 domain of human HUWE1/ARF-BP1

Entity

1. UBM1 domain of human HUWE1/ARF-BP1 (polymer, Thiol state: not present), 53 monomers, 5659.146 Da Detail

TSSEEEDPLA GISLPEGVDP SFLAALPDDI RREVLQNQLG IRPPTRTAPS TNS

Formula weight

5659.146 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 89.8 %, Completeness (bb): 90.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.8 % (518 of 577)	91.1 % (275 of 302)	88.0 % (198 of 225)	90.0 % (45 of 50)
Backbone	90.5 % (275 of 304)	93.1 % (95 of 102)	88.5 % (138 of 156)	91.3 % (42 of 46)
Sidechain	89.8 % (290 of 323)	90.0 % (180 of 200)	89.9 % (107 of 119)	75.0 % (3 of 4)
Aromatic	60.0 % (6 of 10)	80.0 % (4 of 5)	40.0 % (2 of 5)
Methyl	90.0 % (54 of 60)	90.0 % (27 of 30)	90.0 % (27 of 30)

1. entity

TSSEEEDPLA GISLPEGVDP SFLAALPDDI RREVLQNQLG IRPPTRTAPS TNS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 2.8 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.8 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.44 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MUL, Strand ID: A Detail

Release date

2015-09-13

Citation

Solution structure of Ubiquitin Binding Motif of human Arf-bp1
Khatun, R., Sheng, Y.
Not known

Related entities 1. UBM1 domain of human HUWE1/ARF-BP1, : 1 : 1 : 1 : 3 entities Detail

Interaction partners 1. UBM1 domain of human HUWE1/ARF-BP1, : 59 interactors Detail

More details for 59 interactors identified by 33 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 3D CCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium chloride	natural abundance		300 mM
3	potassium chloride	natural abundance		2.7 mM
4	sodium phosphate	natural abundance		10 mM
5	potassium phosphate	natural abundance		2 mM
6	CHAPS	natural abundance		0.05 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25219_2mul.nef
Input source #2: Coordindates	2mul.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	Error

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

------2960------2970------2980------2990------3000---
TSSEEEDPLAGISLPEGVDPSFLAALPDDIRREVLQNQLGIRPPTRTAPSTNS
|||||||||||||||||||||||||||||||||||||||||||||||||||||
TSSEEEDPLAGISLPEGVDPSFLAALPDDIRREVLQNQLGIRPPTRTAPSTNS
--------10--------20--------30--------40--------50---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	53	0	0	100.0

Content subtype: combined_25219_2mul.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	457		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1036 (1)	noe	90.6 (chain: A, length: 53)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	22 (1)	hbond	32.1 (chain: A, length: 53)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	72 (72)	.	94.3 (chain: A, length: 53)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 90.6%
- Total number of restraints: 1036
- Weight of restraints: 1.0 (1036)
- Potential type of restraints: square-well-parabolic (1036)
- Range of distance target values: 2.25, 3.9 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 32.1%
  - Total number of restraints: 22
  - Weight of restraints: 1.0 (22)
  - Potential type of restraints: square-well-parabolic (22)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 94.3%
- Total number of restraints: 72
- Total number of restraints per polymer type: 72
- Weight of restraints: 1.0 (72)
- Potential type of restraints: square-well-parabolic (72)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PROTEIN/Ubiquitin Binding Motif