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BMRB: 25973

2NBE

Solution structure of V26A mutant of Ubiquitin at pH 2.0

Authors

Surana, P., Das, R.

Assembly

V26A mutant of Ubiquitin at pH 2.0

Entity

1. V26A mutant of Ubiquitin at pH 2.0 (polymer, Thiol state: not present), 76 monomers, 8536.678 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENAKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Formula weight

8536.678 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 78.8 %, Completeness (bb): 94.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.8 % (713 of 905)	70.0 % (333 of 476)	88.8 % (309 of 348)	87.7 % (71 of 81)
Backbone	94.2 % (424 of 450)	93.5 % (145 of 155)	93.7 % (208 of 222)	97.3 % (71 of 73)
Sidechain	67.2 % (353 of 525)	58.3 % (187 of 321)	84.7 % (166 of 196)	0.0 % (0 of 8)
Aromatic	0.0 % (0 of 32)	0.0 % (0 of 16)	0.0 % (0 of 16)
Methyl	83.3 % (80 of 96)	77.1 % (37 of 48)	89.6 % (43 of 48)

1. entity

MQIFVKTLTG KTITLEVEPS DTIENAKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

LACS Plot; CA

Referencing offset: 2.76 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 2.76 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 3.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2016-05-22

Citation

Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR
Surana, P., Das, R.
Protein Sci. (2016), 25, 1438-1450, PubMed 27111887 , DOI 10.1002/pro.2940 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25972 released on 2016-05-22
Title Solution structure of V26A mutant of Ubiquitin at pH 6.0

Related entities 1. V26A mutant of Ubiquitin at pH 2.0, : 1 : 1 : 381 : 340 entities Detail

Interaction partners 1. V26A mutant of Ubiquitin at pH 2.0, : 27 interactors Detail

More details for 27 interactors identified by 16 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz Bruker Avance III HD

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

2 3D HNCO

Instrument

Bruker Avance - 800 MHz Bruker Avance III HD

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

3 3D HNCA

Instrument

Bruker Avance - 800 MHz Bruker Avance III HD

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

4 3D HNCACB

Instrument

Bruker Avance - 800 MHz Bruker Avance III HD

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz Bruker Avance III HD

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

6 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz Bruker Avance III HD

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

7 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz Bruker Avance III HD

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz Bruker Avance III HD

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.0

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

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25973_2nbe.nef
Input source #2: Coordindates	2nbe.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------
MQIFVKTLTGKTITLEVEPSDTIENAKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQIFVKTLTGKTITLEVEPSDTIENAKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_25973_2nbe.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	694		98.7 (chain: A, length: 76)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3693 (1)	noe	98.7 (chain: A, length: 76)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	98 (98)	.	86.8 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 321
  - ¹³C chemical shifts: 302
  - ¹⁵N chemical shifts: 71
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 98.7%
- Total number of restraints: 3464
- Weight of restraints: 1.0 (3464)
- Potential type of restraints: square-well-parabolic (3464)
- Range of distance target values: 1.1, 4.9 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 86.8%
- Total number of restraints: 98
- Total number of restraints per polymer type: 98
- Weight of restraints: 1.0 (98)
- Potential type of restraints: square-well-parabolic (98)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ubiquitin, V26A mutant, late folding intermediate, pH 2.0