BMRBj - BMREntryMaster

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BMRB: 19111

2MUX

USP25

Authors

Shi, L., Zhang, N., Wen, Y.

Assembly

USP25

Entity

1. USP25 (polymer, Thiol state: all free), 166 monomers, 18302.95 Da Detail

MGSSHHHHHH SSGLVPRGSH MTVEQNVLQQ SAAQKHQQTF LNQLREITGI NDTQILQQAL KDSNGNLELA VAFLTAKNAK TPQQEETTYY QTALPGNDRY ISVGSQADTN VIDLTGDDKD DLQRAIALSL AESNRAFRET GITDEEQAIS RVLEASIAEN KACLKR

Formula weight

18302.95 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.8 %, Completeness: 83.8 %, Completeness (bb): 90.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.8 % (1562 of 1863)	81.5 % (787 of 966)	86.3 % (611 of 708)	86.8 % (164 of 189)
Backbone	90.6 % (897 of 990)	87.9 % (297 of 338)	91.8 % (449 of 489)	92.6 % (151 of 163)
Sidechain	78.5 % (809 of 1030)	78.0 % (490 of 628)	81.4 % (306 of 376)	50.0 % (13 of 26)
Aromatic	0.0 % (0 of 86)	0.0 % (0 of 43)	0.0 % (0 of 43)
Methyl	95.2 % (179 of 188)	94.7 % (89 of 94)	95.7 % (90 of 94)

1. USP25

MGSSHHHHHH SSGLVPRGSH MTVEQNVLQQ SAAQKHQQTF LNQLREITGI NDTQILQQAL KDSNGNLELA VAFLTAKNAK TPQQEETTYY QTALPGNDRY ISVGSQADTN VIDLTGDDKD DLQRAIALSL AESNRAFRET GITDEEQAIS RVLEASIAEN KACLKR

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	USP25	[U-99% 13C; U-99% 15N]	0.6 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

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

#	Name	Isotope labeling	Concentration
4	USP25	[U-99% 15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	USP25	[U-99% 13C]		0.8 mM
8	D2O	natural abundance		100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	na	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	na	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	na	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	na	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	na	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	na	indirect	0.1013291

Referencing offset: 0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	na	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	na	indirect	0.1013291

Referencing offset: 0.25 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-08-15

Citation

¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of the N-terminal ubiquitin-binding domains of USP25
Shi, L., Wen, Y., Zhang, N.
Biomol. NMR Assign. (2014), 8, 255-258, PubMed 23754700 , DOI 10.1007/s12104-013-9495-1 , Abstract

Related entities 1. USP25, : 1 : 5 : 4 entities Detail

Interaction partners 1. USP25, : 9 interactors Detail

More details for 9 interactors identified by 5 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	USP25	[U-99% 13C; U-99% 15N]	0.6 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	USP25	[U-99% 13C]		0.8 mM
8	D2O	natural abundance		100 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	USP25	[U-99% 13C; U-99% 15N]	0.6 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	USP25	[U-99% 13C; U-99% 15N]	0.6 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	USP25	[U-99% 13C; U-99% 15N]	0.6 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	USP25	[U-99% 13C; U-99% 15N]	0.6 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

7 3D HCACO

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	USP25	[U-99% 13C; U-99% 15N]	0.6 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	USP25	[U-99% 13C]		0.8 mM
8	D2O	natural abundance		100 %

9 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	USP25	[U-99% 13C]		0.8 mM
8	D2O	natural abundance		100 %

10 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	Concentration
4	USP25	[U-99% 15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 3D HBHA(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	Concentration
4	USP25	[U-99% 15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	USP25	[U-99% 13C]		0.8 mM
8	D2O	natural abundance		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19111_2mux.nef
Input source #2: Coordindates	2mux.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
MGSSHHHHHHSSGLVPRGSHMTVEQNVLQQSAAQKHQQTFLNQLREITGINDTQILQQALKDSNGNLELAVAFLTAKNAKTPQQEETTYYQTALPGNDRY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMTVEQNVLQQSAAQKHQQTFLNQLREITGINDTQILQQALKDSNGNLELAVAFLTAKNAKTPQQEETTYYQTALPGNDRY
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--------90-------100-------110-------120-------130-------140------
ISVGSQADTNVIDLTGDDKDDLQRAIALSLAESNRAFRETGITDEEQAISRVLEASIAENKACLKR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ISVGSQADTNVIDLTGDDKDDLQRAIALSLAESNRAFRETGITDEEQAISRVLEASIAENKACLKR
-------110-------120-------130-------140-------150-------160------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	166	0	0	100.0

Content subtype: combined_19111_2mux.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1552		91.0 (chain: A, length: 166)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1978 (1)	noe	84.9 (chain: A, length: 166)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	82 (1)	hbond	36.7 (chain: A, length: 166)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	126 (126)	.	41.6 (chain: A, length: 166)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 91.0%
- Total number of assignments
  - ¹H chemical shifts: 787
  - ¹³C chemical shifts: 603
  - ¹⁵N chemical shifts: 162
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	966	787	81.5
¹³C chemical shifts	708	603	85.2
¹⁵N chemical shifts	197	162	82.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	338	300	88.8
¹³C chemical shifts	332	301	90.7
¹⁵N chemical shifts	163	150	92.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	628	487	77.5
¹³C chemical shifts	376	302	80.3
¹⁵N chemical shifts	34	12	35.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	90	93.8
¹³C chemical shifts	96	90	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	0	0.0
¹³C chemical shifts	43	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 84.9%
- Total number of restraints: 1959
- Weight of restraints: 1.0 (1959)
- Potential type of restraints: square-well-parabolic (1959)
- Range of distance target values: 2.25, 5.5 (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_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 36.7%
  - Total number of restraints: 82
  - Weight of restraints: 1.0 (82)
  - Potential type of restraints: square-well-parabolic (82)
  - Range of distance target values: 2.15, 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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 41.6%
- Total number of restraints: 126
- Total number of restraints per polymer type: 126
- Weight of restraints: 1.0 (126)
- Potential type of restraints: square-well-parabolic (126)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

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Found 1 Document (0.897 seconds)

BMRB: 19111

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. USP25, : 1 : 5 : 4 entities Detail

Interaction partners 1. USP25, : 9 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail