BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	76.1 % (1005 of 1320)	81.8 % (565 of 691)	65.7 % (333 of 507)	87.7 % (107 of 122)
Backbone	77.6 % (528 of 680)	92.0 % (218 of 237)	62.2 % (206 of 331)	92.9 % (104 of 112)
Sidechain	76.7 % (570 of 743)	76.4 % (347 of 454)	78.9 % (220 of 279)	30.0 % (3 of 10)
Aromatic	2.6 % (2 of 76)	2.6 % (1 of 38)	0.0 % (0 of 37)	100.0 % (1 of 1)
Methyl	96.7 % (116 of 120)	96.7 % (58 of 60)	96.7 % (58 of 60)

1. Ubiquitin/UIM fusion protein

MHHHHHHGEF QIFAKTLTGK TITLEVESSD TIDNVKSKIQ DKEGIPPDQQ RLIWAGKQLE DGRTLSDYNI QRESTLHLVL RLRGGSMGGA ADEEELIRKA IELSLKESRN SGGY

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
7	Ubiquitin/UIM fusion protein	[U-100% 15N]	1.1 mM
8	sodium azide	natural abundance	3 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6, Details acrylamide/N,N'-methylenebisacrylamide gel 83:1

#	Name	Isotope labeling	Concentration
13	Ubiquitin/UIM fusion protein	[U-100% 15N]	0.5 mM
14	sodium azide	natural abundance	3 mM
15	sodium phosphate	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM
17	H2O	natural abundance	95 %
18	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514414
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 2.59 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514414
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 2.59 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514414
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 6 Detail

Protein Blocks Logo

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

Release date

2010-02-10

Citation 1

Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain
Sgourakis, N.G., Patel, M.M., Garcia, A.E., Makhatadze, G.I., McCallum, S.A.
J. Mol. Biol. (2010), 396, 1128-1144, PubMed 20053359 , DOI 10.1016/j.jmb.2009.12.052 , Abstract

Show more 1 citaion

Citation 2

Folding cooperativity and dynamics of a Ubiquitin/UIM fusion protein by NMR, DSC, CD, fluorescence experiments and MD simulations
Patel, M.M., Sgourakis, N.G., Streicher, W.W., McCallum, S.A., Garcia, A.E., Makhatadze, G.I.
Not known

Hide non-primary 1 citaion

Related entities 1. Ubiquitin/UIM fusion protein, : 1 : 9 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
7	Ubiquitin/UIM fusion protein	[U-100% 15N]	1.1 mM
8	sodium azide	natural abundance	3 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

3 3D HN(CO)CACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

4 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
7	Ubiquitin/UIM fusion protein	[U-100% 15N]	1.1 mM
8	sodium azide	natural abundance	3 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

7 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

8 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

9 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

10 2D HN-IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6, Details acrylamide/N,N'-methylenebisacrylamide gel 83:1

#	Name	Isotope labeling	Concentration
13	Ubiquitin/UIM fusion protein	[U-100% 15N]	0.5 mM
14	sodium azide	natural abundance	3 mM
15	sodium phosphate	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM
17	H2O	natural abundance	95 %
18	D2O	natural abundance	5 %

11 3D 1H-15N TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
7	Ubiquitin/UIM fusion protein	[U-100% 15N]	1.1 mM
8	sodium azide	natural abundance	3 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

13 3D (H)C(CCO)NH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
1	Ubiquitin/UIM fusion protein	[U-100% 13C; U-100% 15N]	1.24 mM
2	sodium azide	natural abundance	3 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

14 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6, Details acrylamide/N,N'-methylenebisacrylamide gel 83:1

#	Name	Isotope labeling	Concentration
13	Ubiquitin/UIM fusion protein	[U-100% 15N]	0.5 mM
14	sodium azide	natural abundance	3 mM
15	sodium phosphate	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM
17	H2O	natural abundance	95 %
18	D2O	natural abundance	5 %

15 2D HN-IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6

#	Name	Isotope labeling	Concentration
7	Ubiquitin/UIM fusion protein	[U-100% 15N]	1.1 mM
8	sodium azide	natural abundance	3 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16114_2kdi.nef
Input source #2: Coordindates	2kdi.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
MHHHHHHGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIRKA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIRKA

-------110----
IELSLKESRNSGGY
||||||||||||||
IELSLKESRNSGGY

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	114	0	0	100.0

Content subtype: combined_16114_2kdi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	993		95.6 (chain: A, length: 114)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	2896 (1)	noe	92.1 (chain: A, length: 114)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	46 (1)	hbond	32.5 (chain: A, length: 114)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	158 (158)	.	89.5 (chain: A, length: 114)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	71 (71)	.	62.3 (chain: A, length: 114)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 95.6%
- Total number of assignments
  - ¹H chemical shifts: 564
  - ¹³C chemical shifts: 324
  - ¹⁵N chemical shifts: 105
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	691	564	81.6
¹³C chemical shifts	507	324	63.9
¹⁵N chemical shifts	129	105	81.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	237	220	92.8
¹³C chemical shifts	228	105	46.1
¹⁵N chemical shifts	112	104	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	454	344	75.8
¹³C chemical shifts	279	219	78.5
¹⁵N chemical shifts	17	1	5.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	60	96.8
¹³C chemical shifts	62	60	96.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	1	2.6
¹³C chemical shifts	37	0	0.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 92.1%
- Total number of restraints: 2896
- Weight of restraints: 1.0 (2896)
- Potential type of restraints: square-well-parabolic (2896)
- Range of distance target values: 1.74, 3.25 (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_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 32.5%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: square-well-parabolic (46)
  - Range of distance target values: 1.95, 2.9 (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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 89.5%
- Total number of restraints: 158
- Total number of restraints per polymer type: 158
- Weight of restraints: 1.0 (158)
- Potential type of restraints: square-well-parabolic (158)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 62.3%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MHHHHHHGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIRKA
         |||||||    ||||||||||||| |||| ||||||  |||||||||| ||| |||||||| ||||| ||              |||||||
.........FQIFAKT....TITLEVESSDTID.VKSK.QDKEGI..DQQRLIWAGK.LED.RTLSDYNI.RESTL.LV..............EELIRKA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110----
IELSLKESRNSGGY
||||||        
IELSLK        
------

Total number of restraints: 71
Potential type of restraints: undefined (71)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords protein domain interface, Ubiquitin, Ubiquitin Interacting Motif, UIM

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Found 1 Document (0.686 seconds)

BMRB: 16114

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Ubiquitin/UIM fusion protein, : 1 : 9 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 6 contents Detail